title: kidney cell 566, Lean, 20 weeks

description:
kidney cell 566
039s_O16


title: kidney cell 569, Lean, 20 weeks

status: Public on May 01 2024

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
kidney cell 569
039s_O20

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
For labelling of EC and live cells, the kidney cell suspension was incubated with APC-conjugated anti-CD31 antibody (1:100, 551262, BD Biosciences) and Calcein AM (2 µM, C3099, Thermo Fisher Scientific) for 20 min at RT, then centrifugated as above, supernatant removed, and the cell pellet resuspended in FACS buffer and placed on ice. The SmartSeq2 methodology was used for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: kidney

tag: genotype

value: Lean

tag: disease state

value: control

tag: age

value: 20 weeks


title: MGH229-P9-B06-CD45neg, Smart-seq2

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

country: USA

institute: Massachusetts General Hospital

description: Smartseq2_Oligodendroglioma_processed_TPM.tsv

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7). Statistical analysis was done using R version 4.0.1. We merged the gene expression levels which were calculated by RSEM48 for MGH170 and MGH229 with the ones calculated for the reference samples from Tirosh 2016 (downloaded from https://singlecell.broadinstitute.org/single_cell). Analysis was done mainly using the R package scandal which is freely available at https://github.com/dravishays/scandal.  Gene expression levels were quantified as TPM (transcript-per-million reads).
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

molecule: polyA RNA

organism: Homo sapiens

source_name: Oligodendroglioma single cell, MGH229-CD45neg

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics or stained by Ruby (ThermoFisher, V10309) and sorted into 96 well plates. IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
RNA from single cells or single nucleus was first purified with Agencourt RNAClean XP beads (Beckman Coulter). B65Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq sequencer (Illumina). Multi-omics library (DNA methylome and transcriptome) was generated based on the Smart-RRBS protocol (Chaligne et al, 2021).

tag: treatment (idhi)

value: Yes


title: kidney cell 568, Lean, 20 weeks

description:
kidney cell 568
039s_O2


title: kidney cell 564, Lean, 20 weeks

description:
kidney cell 564
039s_O14


title: MGH229-P9-B04-CD45neg, Smart-seq2

value: Oligodendroglioma single cell, MGH229-CD45neg


title: MGH229-P9-B05-CD45neg, Smart-seq2


title: kidney cell 563, Lean, 20 weeks

description:
kidney cell 563
039s_O13


title: kidney cell 565, Lean, 20 weeks

description:
kidney cell 565
039s_O15


title: MGH229-P9-B03-CD45neg, Smart-seq2


title: kidney cell 576, Lean, 20 weeks

description:
kidney cell 576
039s_O6


title: kidney cell 561, Lean, 20 weeks

description:
kidney cell 561
039s_O11


title: MGH229-P9-B02-CD45neg, Smart-seq2


title: MGH229-P9-B01-CD45neg, Smart-seq2


title: kidney cell 559, Lean, 20 weeks

description:
kidney cell 559
039s_O1


title: MGH229-P9-A12-CD45neg, Smart-seq2


title: kidney cell 560, Lean, 20 weeks

description:
kidney cell 560
039s_O10


title: kidney cell 562, Lean, 20 weeks

description:
kidney cell 562
039s_O12


title: MGH229-P9-A11-CD45neg, Smart-seq2


title: kidney cell 558, Lean, 20 weeks

description:
kidney cell 558
039s_N9


title: MGH229-P9-A09-CD45neg, Smart-seq2


title: MGH229-P9-A06-CD45neg, Smart-seq2


title: kidney cell 557, Lean, 20 weeks

description:
kidney cell 557
039s_N8


title: MGH229-P9-A08-CD45neg, Smart-seq2


title: kidney cell 556, Lean, 20 weeks

description:
kidney cell 556
039s_N7


title: kidney cell 555, Lean, 20 weeks

description:
kidney cell 555
039s_N6


title: MGH229-P9-A05-CD45neg, Smart-seq2


title: kidney cell 554, Lean, 20 weeks

description:
kidney cell 554
039s_N5


title: MGH229-P9-A03-CD45neg, Smart-seq2


title: kidney cell 553, Lean, 20 weeks

description:
kidney cell 553
039s_N4


title: MGH229-P9-A01-CD45neg, Smart-seq2


title: MGH229-P9-A02-CD45neg, Smart-seq2


title: MGH229-P4-H12-CD45neg, Smart-seq2


title: kidney cell 551, Lean, 20 weeks

description:
kidney cell 551
039s_N24


title: kidney cell 552, Lean, 20 weeks

description:
kidney cell 552
039s_N3


title: kidney cell 549, Lean, 20 weeks

description:
kidney cell 549
039s_N2


title: kidney cell 550, Lean, 20 weeks

description:
kidney cell 550
039s_N20


title: kidney cell 548, Lean, 20 weeks

description:
kidney cell 548
039s_N19


title: MGH229-P4-H07-CD45neg, Smart-seq2


title: kidney cell 547, Lean, 20 weeks

description:
kidney cell 547
039s_N18


title: MGH229-P4-H08-CD45neg, Smart-seq2


title: kidney cell 546, Lean, 20 weeks

description:
kidney cell 546
039s_N17


title: MGH229-P4-H10-CD45neg, Smart-seq2


title: MGH229-P4-H06-CD45neg, Smart-seq2


title: kidney cell 545, Lean, 20 weeks

description:
kidney cell 545
039s_N16


title: MGH229-P4-H05-CD45neg, Smart-seq2


title: MGH229-P4-H03-CD45neg, Smart-seq2


title: kidney cell 543, Lean, 20 weeks

description:
kidney cell 543
039s_N14


title: MGH229-P9-A04-CD45neg, Smart-seq2


title: kidney cell 542, Lean, 20 weeks

description:
kidney cell 542
039s_N13


title: MGH229-P4-H02-CD45neg, Smart-seq2


title: MGH229-P4-H01-CD45neg, Smart-seq2


title: kidney cell 541, Lean, 20 weeks

description:
kidney cell 541
039s_N12


title: kidney cell 540, Lean, 20 weeks

description:
kidney cell 540
039s_N11


title: kidney cell 539, Lean, 20 weeks

description:
kidney cell 539
039s_N1


title: MGH229-P4-G11-CD45neg, Smart-seq2


title: MGH229-P4-G12-CD45neg, Smart-seq2


title: kidney cell 538, Lean, 20 weeks

description:
kidney cell 538
039s_M9


title: MGH229-P4-G10-CD45neg, Smart-seq2


title: MGH229-P4-G09-CD45neg, Smart-seq2


title: kidney cell 537, Lean, 20 weeks

description:
kidney cell 537
039s_M8


title: kidney cell 536, Lean, 20 weeks

description:
kidney cell 536
039s_M7


title: MGH229-P4-G07-CD45neg, Smart-seq2


title: MGH229-P4-G05-CD45neg, Smart-seq2


title: MGH229-P4-G04-CD45neg, Smart-seq2


title: MGH229-P4-G03-CD45neg, Smart-seq2


title: kidney cell 534, Lean, 20 weeks

description:
kidney cell 534
039s_M5


title: kidney cell 532, Lean, 20 weeks

description:
kidney cell 532
039s_M3


title: MGH229-P4-G06-CD45neg, Smart-seq2


title: kidney cell 544, Lean, 20 weeks

description:
kidney cell 544
039s_N15


title: kidney cell 533, Lean, 20 weeks

description:
kidney cell 533
039s_M4


title: MGH229-P4-G02-CD45neg, Smart-seq2


title: kidney cell 530, Lean, 20 weeks

description:
kidney cell 530
039s_M22


title: kidney cell 529, Lean, 20 weeks

description:
kidney cell 529
039s_M21


title: MGH229-P4-H04-CD45neg, Smart-seq2


title: MGH229-P4-G01-CD45neg, Smart-seq2


title: MGH229-P4-F11-CD45neg, Smart-seq2


title: MGH229-P4-F10-CD45neg, Smart-seq2


title: MGH229-P4-F09-CD45neg, Smart-seq2


title: kidney cell 527, Lean, 20 weeks

description:
kidney cell 527
039s_M2


title: MGH229-P4-F08-CD45neg, Smart-seq2


title: kidney cell 526, Lean, 20 weeks

description:
kidney cell 526
039s_M19


title: MGH229-P4-F06-CD45neg, Smart-seq2


title: kidney cell 535, Lean, 20 weeks

description:
kidney cell 535
039s_M6


title: kidney cell 524, Lean, 20 weeks

description:
kidney cell 524
039s_M16


title: MGH229-P4-F05-CD45neg, Smart-seq2


title: kidney cell 522, Lean, 20 weeks

description:
kidney cell 522
039s_M14


title: kidney cell 523, Lean, 20 weeks

description:
kidney cell 523
039s_M15


title: kidney cell 531, Lean, 20 weeks

description:
kidney cell 531
039s_M24


title: MGH229-P4-F04-CD45neg, Smart-seq2


title: kidney cell 520, Lean, 20 weeks

description:
kidney cell 520
039s_M12


title: MGH229-P4-F03-CD45neg, Smart-seq2


title: kidney cell 521, Lean, 20 weeks

description:
kidney cell 521
039s_M13


title: MGH229-P4-E11-CD45neg, Smart-seq2


title: MGH229-P4-E12-CD45neg, Smart-seq2


title: MGH229-P4-E10-CD45neg, Smart-seq2


title: MGH229-P4-F01-CD45neg, Smart-seq2


title: kidney cell 518, Lean, 20 weeks

description:
kidney cell 518
039s_M1


title: kidney cell 528, Lean, 20 weeks

description:
kidney cell 528
039s_M20


title: MGH229-P4-E09-CD45neg, Smart-seq2


title: MGH229-P4-E07-CD45neg, Smart-seq2


title: kidney cell 517, Lean, 20 weeks

description:
kidney cell 517
039s_L9


title: kidney cell 516, Lean, 20 weeks

description:
kidney cell 516
039s_L8


title: MGH229-P4-F07-CD45neg, Smart-seq2


title: MGH229-P4-E08-CD45neg, Smart-seq2


title: kidney cell 515, Lean, 20 weeks

description:
kidney cell 515
039s_L7


title: kidney cell 514, Lean, 20 weeks

description:
kidney cell 514
039s_L6


title: kidney cell 513, Lean, 20 weeks

description:
kidney cell 513
039s_L5


title: MGH229-P4-E02-CD45neg, Smart-seq2


title: kidney cell 510, Lean, 20 weeks

description:
kidney cell 510
039s_L23


title: kidney cell 525, Lean, 20 weeks

description:
kidney cell 525
039s_M17


title: MGH229-P4-E06-CD45neg, Smart-seq2


title: kidney cell 519, Lean, 20 weeks

description:
kidney cell 519
039s_M11


title: kidney cell 509, Lean, 20 weeks

description:
kidney cell 509
039s_L22


title: MGH229-P4-E05-CD45neg, Smart-seq2


title: kidney cell 512, Lean, 20 weeks

description:
kidney cell 512
039s_L4


title: MGH229-P4-D12-CD45neg, Smart-seq2


title: kidney cell 511, Lean, 20 weeks

description:
kidney cell 511
039s_L24


title: MGH229-P4-E04-CD45neg, Smart-seq2


title: MGH229-P4-D11-CD45neg, Smart-seq2


title: kidney cell 507, Lean, 20 weeks

description:
kidney cell 507
039s_L20


title: MGH229-P4-D10-CD45neg, Smart-seq2


title: MGH229-P4-D09-CD45neg, Smart-seq2


title: MGH229-P4-D07-CD45neg, Smart-seq2


title: kidney cell 505, Lean, 20 weeks

description:
kidney cell 505
039s_L19


title: kidney cell 506, Lean, 20 weeks

description:
kidney cell 506
039s_L2


title: MGH229-P4-D06-CD45neg, Smart-seq2


title: kidney cell 504, Lean, 20 weeks

description:
kidney cell 504
039s_L18


title: kidney cell 503, Lean, 20 weeks

description:
kidney cell 503
039s_L17


title: MGH229-P4-D05-CD45neg, Smart-seq2


title: MGH229-P4-D03-CD45neg, Smart-seq2


title: kidney cell 501, Lean, 20 weeks

description:
kidney cell 501
039s_L15


title: kidney cell 502, Lean, 20 weeks

description:
kidney cell 502
039s_L16


title: kidney cell 500, Lean, 20 weeks

description:
kidney cell 500
039s_L14


title: kidney cell 499, Lean, 20 weeks

description:
kidney cell 499
039s_L13


title: kidney cell 508, Lean, 20 weeks

description:
kidney cell 508
039s_L21


title: MGH229-P4-D04-CD45neg, Smart-seq2


title: MGH229-P4-C12-CD45neg, Smart-seq2


title: MGH229-P4-D01-CD45neg, Smart-seq2


title: MGH229-P4-C11-CD45neg, Smart-seq2


title: kidney cell 497, Lean, 20 weeks

description:
kidney cell 497
039s_L11


title: MGH229-P4-C10-CD45neg, Smart-seq2


title: kidney cell 496, Lean, 20 weeks

description:
kidney cell 496
039s_K9


title: MGH229-P4-C09-CD45neg, Smart-seq2


title: kidney cell 495, Lean, 20 weeks

description:
kidney cell 495
039s_K8


title: MGH229-P4-C08-CD45neg, Smart-seq2


title: kidney cell 494, Lean, 20 weeks

description:
kidney cell 494
039s_K7


title: kidney cell 493, Lean, 20 weeks

description:
kidney cell 493
039s_K6


title: MGH229-P4-C07-CD45neg, Smart-seq2


title: MGH229-P4-C05-CD45neg, Smart-seq2


title: MGH229-P4-D02-CD45neg, Smart-seq2


title: MGH229-P4-C02-CD45neg, Smart-seq2


title: kidney cell 491, Lean, 20 weeks

description:
kidney cell 491
039s_K4


title: kidney cell 492, Lean, 20 weeks

description:
kidney cell 492
039s_K5


title: kidney cell 490, Lean, 20 weeks

description:
kidney cell 490
039s_K3


title: kidney cell 489, Lean, 20 weeks

description:
kidney cell 489
039s_K24


title: MGH229-P4-B12-CD45neg, Smart-seq2


title: MGH229-P4-C01-CD45neg, Smart-seq2


title: MGH229-P4-B11-CD45neg, Smart-seq2


title: kidney cell 487, Lean, 20 weeks

description:
kidney cell 487
039s_K22


title: MGH229-P4-B09-CD45neg, Smart-seq2


title: MGH229-P4-B08-CD45neg, Smart-seq2


title: MGH229-P4-B04-CD45neg, Smart-seq2


title: kidney cell 485, Lean, 20 weeks

description:
kidney cell 485
039s_K20


title: kidney cell 483, Lean, 20 weeks

description:
kidney cell 483
039s_K19


title: kidney cell 484, Lean, 20 weeks

description:
kidney cell 484
039s_K2


title: MGH229-P4-B07-CD45neg, Smart-seq2


title: kidney cell 482, Lean, 20 weeks

description:
kidney cell 482
039s_K18


title: MGH229-P4-B05-CD45neg, Smart-seq2


title: MGH229-P4-B01-CD45neg, Smart-seq2


title: MGH229-P4-B03-CD45neg, Smart-seq2


title: kidney cell 481, Lean, 20 weeks

description:
kidney cell 481
039s_K16


title: MGH229-P4-A12-CD45neg, Smart-seq2


title: kidney cell 480, Lean, 20 weeks

description:
kidney cell 480
039s_K15


title: kidney cell 479, Lean, 20 weeks

description:
kidney cell 479
039s_K14


title: kidney cell 488, Lean, 20 weeks

description:
kidney cell 488
039s_K23


title: MGH229-P4-A08-CD45neg, Smart-seq2


title: MGH229-P4-A07-CD45neg, Smart-seq2


title: MGH229-P4-A09-CD45neg, Smart-seq2


title: kidney cell 476, Lean, 20 weeks

description:
kidney cell 476
039s_K11


title: MGH229-P4-A03-CD45neg, Smart-seq2


title: kidney cell 474, Lean, 20 weeks

description:
kidney cell 474
039s_J9


title: MGH229-P4-A06-CD45neg, Smart-seq2


title: kidney cell 486, Lean, 20 weeks

description:
kidney cell 486
039s_K21


title: kidney cell 475, Lean, 20 weeks

description:
kidney cell 475
039s_K10


title: kidney cell 477, Lean, 20 weeks

description:
kidney cell 477
039s_K12


title: MGH229-P4-A02-CD45neg, Smart-seq2


title: MGH229-P4-B06-CD45neg, Smart-seq2


title: kidney cell 473, Lean, 20 weeks

description:
kidney cell 473
039s_J8


title: MGH229-P4-A01-CD45neg, Smart-seq2


title: kidney cell 472, Lean, 20 weeks

description:
kidney cell 472
039s_J7


title: kidney cell 471, Lean, 20 weeks

description:
kidney cell 471
039s_J6


title: MGH229-P2-H11-CD45neg, Smart-seq2


title: MGH229-P2-H12-CD45neg, Smart-seq2


title: kidney cell 470, Lean, 20 weeks

description:
kidney cell 470
039s_J5


title: MGH229-P2-H09-CD45neg, Smart-seq2


title: kidney cell 478, Lean, 20 weeks

description:
kidney cell 478
039s_K13


title: kidney cell 465, Lean, 20 weeks

description:
kidney cell 465
039s_J22


title: MGH229-P2-H10-CD45neg, Smart-seq2


title: MGH229-P2-H04-CD45neg, Smart-seq2


title: MGH229-P2-H03-CD45neg, Smart-seq2


title: kidney cell 461, Lean, 20 weeks

description:
kidney cell 461
039s_J19


title: kidney cell 462, Lean, 20 weeks

description:
kidney cell 462
039s_J2


title: MGH229-P2-H02-CD45neg, Smart-seq2


title: MGH229-P2-G12-CD45neg, Smart-seq2


title: MGH229-P2-H08-CD45neg, Smart-seq2


title: kidney cell 466, Lean, 20 weeks

description:
kidney cell 466
039s_J23


title: kidney cell 469, Lean, 20 weeks

description:
kidney cell 469
039s_J4


title: kidney cell 467, Lean, 20 weeks

description:
kidney cell 467
039s_J24


title: kidney cell 468, Lean, 20 weeks

description:
kidney cell 468
039s_J3


title: kidney cell 464, Lean, 20 weeks

description:
kidney cell 464
039s_J21


title: MGH229-P2-H07-CD45neg, Smart-seq2


title: MGH229-P2-H05-CD45neg, Smart-seq2


title: kidney cell 460, Lean, 20 weeks

description:
kidney cell 460
039s_J18


title: kidney cell 457, Lean, 20 weeks

description:
kidney cell 457
039s_J14


title: MGH229-P2-G11-CD45neg, Smart-seq2


title: kidney cell 498, Lean, 20 weeks

description:
kidney cell 498
039s_L12


title: kidney cell 463, Lean, 20 weeks

description:
kidney cell 463
039s_J20


title: kidney cell 459, Lean, 20 weeks

description:
kidney cell 459
039s_J17


title: kidney cell 455, Lean, 20 weeks

description:
kidney cell 455
039s_J12


title: MGH229-P2-G08-CD45neg, Smart-seq2


title: MGH229-P2-H01-CD45neg, Smart-seq2


title: MGH229-P2-G07-CD45neg, Smart-seq2


title: MGH229-P2-H06-CD45neg, Smart-seq2


title: MGH229-P2-G10-CD45neg, Smart-seq2


title: kidney cell 454, Lean, 20 weeks

description:
kidney cell 454
039s_J11


title: MGH229-P2-G05-CD45neg, Smart-seq2


title: kidney cell 451, Lean, 20 weeks

description:
kidney cell 451
039s_I9


title: MGH229-P2-G09-CD45neg, Smart-seq2


title: kidney cell 456, Lean, 20 weeks

description:
kidney cell 456
039s_J13


title: kidney cell 450, Lean, 20 weeks

description:
kidney cell 450
039s_I8


title: MGH229-P2-G06-CD45neg, Smart-seq2


title: kidney cell 453, Lean, 20 weeks

description:
kidney cell 453
039s_J10


title: MGH229-P2-G01-CD45neg, Smart-seq2


title: kidney cell 449, Lean, 20 weeks

description:
kidney cell 449
039s_I7


title: kidney cell 452, Lean, 20 weeks

description:
kidney cell 452
039s_J1


title: MGH229-P2-G02-CD45neg, Smart-seq2


title: MGH229-P2-F12-CD45neg, Smart-seq2


title: MGH229-P2-G04-CD45neg, Smart-seq2


title: kidney cell 448, Lean, 20 weeks

description:
kidney cell 448
039s_I6


title: kidney cell 458, Lean, 20 weeks

description:
kidney cell 458
039s_J15


title: kidney cell 445, Lean, 20 weeks

description:
kidney cell 445
039s_I3


title: MGH229-P2-F11-CD45neg, Smart-seq2


title: MGH229-P2-F10-CD45neg, Smart-seq2


title: kidney cell 444, Lean, 20 weeks

description:
kidney cell 444
039s_I24


title: MGH229-P2-F08-CD45neg, Smart-seq2


title: kidney cell 442, Lean, 20 weeks

description:
kidney cell 442
039s_I22


title: MGH229-P2-F07-CD45neg, Smart-seq2


title: MGH229-P2-F09-CD45neg, Smart-seq2


title: kidney cell 441, Lean, 20 weeks

description:
kidney cell 441
039s_I21


title: kidney cell 440, Lean, 20 weeks

description:
kidney cell 440
039s_I20


title: MGH229-P2-G03-CD45neg, Smart-seq2


title: MGH229-P2-F04-CD45neg, Smart-seq2


title: kidney cell 439, Lean, 20 weeks

description:
kidney cell 439
039s_I2


title: kidney cell 438, Lean, 20 weeks

description:
kidney cell 438
039s_I19


title: MGH229-P2-F05-CD45neg, Smart-seq2


title: MGH229-P2-F03-CD45neg, Smart-seq2


title: MGH229-P2-F02-CD45neg, Smart-seq2


title: kidney cell 437, Lean, 20 weeks

description:
kidney cell 437
039s_I18


title: kidney cell 447, Lean, 20 weeks

description:
kidney cell 447
039s_I5


title: kidney cell 436, Lean, 20 weeks

description:
kidney cell 436
039s_I17


title: MGH229-P2-F01-CD45neg, Smart-seq2


title: kidney cell 446, Lean, 20 weeks

description:
kidney cell 446
039s_I4


title: kidney cell 435, Lean, 20 weeks

description:
kidney cell 435
039s_I16


title: MGH229-P2-E11-CD45neg, Smart-seq2


title: MGH229-P2-E12-CD45neg, Smart-seq2


title: kidney cell 434, Lean, 20 weeks

description:
kidney cell 434
039s_I15


title: MGH229-P2-E10-CD45neg, Smart-seq2


title: kidney cell 433, Lean, 20 weeks

description:
kidney cell 433
039s_I14


title: kidney cell 431, Lean, 20 weeks

description:
kidney cell 431
039s_I12


title: MGH229-P2-F06-CD45neg, Smart-seq2


title: MGH229-P2-E09-CD45neg, Smart-seq2


title: kidney cell 443, Lean, 20 weeks

description:
kidney cell 443
039s_I23


title: MGH229-P2-E08-CD45neg, Smart-seq2


title: kidney cell 430, Lean, 20 weeks

description:
kidney cell 430
039s_I11


title: MGH229-P2-E06-CD45neg, Smart-seq2


title: kidney cell 428, Lean, 20 weeks

description:
kidney cell 428
039s_H9


title: kidney cell 429, Lean, 20 weeks

description:
kidney cell 429
039s_I1


title: MGH229-P2-E07-CD45neg, Smart-seq2


title: MGH229-P2-E05-CD45neg, Smart-seq2


title: MGH229-P2-E04-CD45neg, Smart-seq2


title: kidney cell 427, Lean, 20 weeks

description:
kidney cell 427
039s_H7


title: MGH229-P2-E03-CD45neg, Smart-seq2


title: MGH229-P2-E01-CD45neg, Smart-seq2


title: kidney cell 425, Lean, 20 weeks

description:
kidney cell 425
039s_H4


title: kidney cell 426, Lean, 20 weeks

description:
kidney cell 426
039s_H5


title: kidney cell 424, Lean, 20 weeks

description:
kidney cell 424
039s_H3


title: kidney cell 423, Lean, 20 weeks

description:
kidney cell 423
039s_H24


title: MGH229-P2-D12-CD45neg, Smart-seq2


title: MGH229-P2-D10-CD45neg, Smart-seq2


title: MGH229-P2-D09-CD45neg, Smart-seq2


title: kidney cell 422, Lean, 20 weeks

description:
kidney cell 422
039s_H23


title: kidney cell 421, Lean, 20 weeks

description:
kidney cell 421
039s_H22


title: kidney cell 420, Lean, 20 weeks

description:
kidney cell 420
039s_H21


title: kidney cell 432, Lean, 20 weeks

description:
kidney cell 432
039s_I13


title: MGH229-P2-D07-CD45neg, Smart-seq2


title: MGH229-P2-D08-CD45neg, Smart-seq2


title: kidney cell 418, Lean, 20 weeks

description:
kidney cell 418
039s_H2


title: MGH229-P2-D06-CD45neg, Smart-seq2


title: MGH229-P2-D05-CD45neg, Smart-seq2


title: kidney cell 417, Lean, 20 weeks

description:
kidney cell 417
039s_H19


title: kidney cell 419, Lean, 20 weeks

description:
kidney cell 419
039s_H20


title: MGH229-P2-D04-CD45neg, Smart-seq2


title: kidney cell 416, Lean, 20 weeks

description:
kidney cell 416
039s_H18


title: MGH229-P2-D03-CD45neg, Smart-seq2


title: MGH229-P2-D02-CD45neg, Smart-seq2


title: kidney cell 413, Lean, 20 weeks

description:
kidney cell 413
039s_H15


title: MGH229-P2-D01-CD45neg, Smart-seq2


title: kidney cell 415, Lean, 20 weeks

description:
kidney cell 415
039s_H17


title: kidney cell 412, Lean, 20 weeks

description:
kidney cell 412
039s_H14


title: MGH229-P2-C12-CD45neg, Smart-seq2


title: MGH229-P2-D11-CD45neg, Smart-seq2


title: kidney cell 410, Lean, 20 weeks

description:
kidney cell 410
039s_H12


title: MGH229-P2-C10-CD45neg, Smart-seq2


title: MGH229-P2-C09-CD45neg, Smart-seq2


title: MGH229-P2-C11-CD45neg, Smart-seq2


title: kidney cell 408, Lean, 20 weeks

description:
kidney cell 408
039s_H10


title: MGH229-P2-C06-CD45neg, Smart-seq2


title: kidney cell 409, Lean, 20 weeks

description:
kidney cell 409
039s_H11


title: MGH229-P2-C05-CD45neg, Smart-seq2


title: kidney cell 407, Lean, 20 weeks

description:
kidney cell 407
039s_H1


title: MGH229-P2-C08-CD45neg, Smart-seq2


title: kidney cell 406, Lean, 20 weeks

description:
kidney cell 406
039s_G9


title: MGH229-P2-C03-CD45neg, Smart-seq2


title: kidney cell 414, Lean, 20 weeks

description:
kidney cell 414
039s_H16


title: kidney cell 403, Lean, 20 weeks

description:
kidney cell 403
039s_G6


title: MGH229-P2-C01-CD45neg, Smart-seq2


title: kidney cell 402, Lean, 20 weeks

description:
kidney cell 402
039s_G5


title: MGH229-P2-C02-CD45neg, Smart-seq2


title: MGH229-P2-C04-CD45neg, Smart-seq2


title: kidney cell 405, Lean, 20 weeks

description:
kidney cell 405
039s_G8


title: MGH229-P2-B12-CD45neg, Smart-seq2


title: kidney cell 401, Lean, 20 weeks

description:
kidney cell 401
039s_G4


title: kidney cell 400, Lean, 20 weeks

description:
kidney cell 400
039s_G3


title: MGH229-P2-B11-CD45neg, Smart-seq2


title: kidney cell 399, Lean, 20 weeks

description:
kidney cell 399
039s_G24


title: kidney cell 411, Lean, 20 weeks

description:
kidney cell 411
039s_H13


title: MGH229-P2-B08-CD45neg, Smart-seq2


title: MGH229-P2-B10-CD45neg, Smart-seq2


title: kidney cell 398, Lean, 20 weeks

description:
kidney cell 398
039s_G23


title: MGH229-P2-B07-CD45neg, Smart-seq2


title: kidney cell 397, Lean, 20 weeks

description:
kidney cell 397
039s_G22


title: MGH229-P2-B06-CD45neg, Smart-seq2


title: kidney cell 395, Lean, 20 weeks

description:
kidney cell 395
039s_G20


title: kidney cell 404, Lean, 20 weeks

description:
kidney cell 404
039s_G7


title: MGH229-P2-B05-CD45neg, Smart-seq2


title: MGH229-P2-B04-CD45neg, Smart-seq2


title: kidney cell 393, Lean, 20 weeks

description:
kidney cell 393
039s_G19


title: MGH229-P2-B03-CD45neg, Smart-seq2


title: kidney cell 394, Lean, 20 weeks

description:
kidney cell 394
039s_G2


title: MGH229-P2-B02-CD45neg, Smart-seq2


title: kidney cell 392, Lean, 20 weeks

description:
kidney cell 392
039s_G18


title: kidney cell 391, Lean, 20 weeks

description:
kidney cell 391
039s_G17


title: MGH229-P2-B01-CD45neg, Smart-seq2


title: MGH229-P2-A10-CD45neg, Smart-seq2


title: kidney cell 390, Lean, 20 weeks

description:
kidney cell 390
039s_G16


title: MGH229-P2-A12-CD45neg, Smart-seq2


title: MGH229-P2-A11-CD45neg, Smart-seq2


title: kidney cell 387, Lean, 20 weeks

description:
kidney cell 387
039s_G13


title: kidney cell 388, Lean, 20 weeks

description:
kidney cell 388
039s_G14


title: MGH229-P2-A09-CD45neg, Smart-seq2


title: kidney cell 389, Lean, 20 weeks

description:
kidney cell 389
039s_G15


title: MGH229-P2-A07-CD45neg, Smart-seq2


title: kidney cell 383, Lean, 20 weeks

description:
kidney cell 383
039s_F9


title: kidney cell 384, Lean, 20 weeks

description:
kidney cell 384
039s_G1


title: kidney cell 386, Lean, 20 weeks

description:
kidney cell 386
039s_G12


title: kidney cell 382, Lean, 20 weeks

description:
kidney cell 382
039s_F7


title: MGH229-P2-A08-CD45neg, Smart-seq2


title: MGH229-P2-A06-CD45neg, Smart-seq2


title: kidney cell 396, Lean, 20 weeks

description:
kidney cell 396
039s_G21


title: MGH229-P2-A02-CD45neg, Smart-seq2


title: kidney cell 385, Lean, 20 weeks

description:
kidney cell 385
039s_G11


title: kidney cell 380, Lean, 20 weeks

description:
kidney cell 380
039s_F4


title: kidney cell 378, Lean, 20 weeks

description:
kidney cell 378
039s_F24


title: MGH229-P2-A03-CD45neg, Smart-seq2


title: MGH170-P9-H10-CD45neg, Smart-seq2

source_name: Oligodendroglioma single cell, MGH170-CD45neg


title: kidney cell 381, Lean, 20 weeks

description:
kidney cell 381
039s_F5


title: kidney cell 376, Lean, 20 weeks

description:
kidney cell 376
039s_F22


title: MGH170-P9-H04-CD45neg, Smart-seq2

value: Oligodendroglioma single cell, MGH170-CD45neg


title: MGH229-P2-A04-CD45neg, Smart-seq2


title: kidney cell 379, Lean, 20 weeks

description:
kidney cell 379
039s_F3


title: MGH229-P2-A01-CD45neg, Smart-seq2


title: MGH170-P9-H09-CD45neg, Smart-seq2


title: MGH170-P9-H11-CD45neg, Smart-seq2


title: MGH170-P9-H03-CD45neg, Smart-seq2


title: kidney cell 377, Lean, 20 weeks

description:
kidney cell 377
039s_F23


title: kidney cell 375, Lean, 20 weeks

description:
kidney cell 375
039s_F21


title: kidney cell 371, Lean, 20 weeks

description:
kidney cell 371
039s_F18


title: MGH170-P9-H07-CD45neg, Smart-seq2


title: kidney cell 374, Lean, 20 weeks

description:
kidney cell 374
039s_F20


title: MGH170-P9-G12-CD45neg, Smart-seq2


title: MGH170-P9-G09-CD45neg, Smart-seq2


title: MGH170-P9-H05-CD45neg, Smart-seq2


title: MGH229-P2-A05-CD45neg, Smart-seq2


title: kidney cell 373, Lean, 20 weeks

description:
kidney cell 373
039s_F2


title: kidney cell 366, Lean, 20 weeks

description:
kidney cell 366
039s_F13


title: kidney cell 365, Lean, 20 weeks

description:
kidney cell 365
039s_F11


title: kidney cell 372, Lean, 20 weeks

description:
kidney cell 372
039s_F19


title: MGH170-P9-H02-CD45neg, Smart-seq2


title: kidney cell 370, Lean, 20 weeks

description:
kidney cell 370
039s_F17


title: kidney cell 364, Lean, 20 weeks

description:
kidney cell 364
039s_E9


title: MGH170-P9-G01-CD45neg, Smart-seq2


title: MGH170-P9-F11-CD45neg, Smart-seq2


title: kidney cell 363, Lean, 20 weeks

description:
kidney cell 363
039s_E8


title: kidney cell 369, Lean, 20 weeks

description:
kidney cell 369
039s_F16


title: MGH170-P9-G10-CD45neg, Smart-seq2


title: MGH170-P9-E11-CD45neg, Smart-seq2


title: kidney cell 368, Lean, 20 weeks

description:
kidney cell 368
039s_F15


title: kidney cell 356, Lean, 20 weeks

description:
kidney cell 356
039s_E20


title: kidney cell 367, Lean, 20 weeks

description:
kidney cell 367
039s_F14


title: MGH170-P9-G05-CD45neg, Smart-seq2


title: MGH170-P9-E10-CD45neg, Smart-seq2


title: MGH170-P9-G04-CD45neg, Smart-seq2


title: MGH170-P9-F07-CD45neg, Smart-seq2


title: kidney cell 354, Lean, 20 weeks

description:
kidney cell 354
039s_E19


title: MGH170-P9-F04-CD45neg, Smart-seq2


title: kidney cell 362, Lean, 20 weeks

description:
kidney cell 362
039s_E7


title: MGH170-P9-F05-CD45neg, Smart-seq2


title: kidney cell 359, Lean, 20 weeks

description:
kidney cell 359
039s_E4


title: MGH170-P9-E05-CD45neg, Smart-seq2


title: kidney cell 361, Lean, 20 weeks

description:
kidney cell 361
039s_E6


title: MGH170-P9-E06-CD45neg, Smart-seq2


title: kidney cell 358, Lean, 20 weeks

description:
kidney cell 358
039s_E22


title: kidney cell 353, Lean, 20 weeks

description:
kidney cell 353
039s_E18


title: MGH170-P9-F01-CD45neg, Smart-seq2


title: MGH170-P9-F02-CD45neg, Smart-seq2


title: MGH170-P9-G02-CD45neg, Smart-seq2


title: kidney cell 357, Lean, 20 weeks

description:
kidney cell 357
039s_E21


title: MGH170-P9-D08-CD45neg, Smart-seq2


title: kidney cell 355, Lean, 20 weeks

description:
kidney cell 355
039s_E2


title: MGH170-P9-D05-CD45neg, Smart-seq2


title: kidney cell 352, Lean, 20 weeks

description:
kidney cell 352
039s_E17


title: MGH170-P9-F10-CD45neg, Smart-seq2


title: MGH170-P9-D04-CD45neg, Smart-seq2


title: kidney cell 351, Lean, 20 weeks

description:
kidney cell 351
039s_E16


title: kidney cell 360, Lean, 20 weeks

description:
kidney cell 360
039s_E5


title: kidney cell 349, Lean, 20 weeks

description:
kidney cell 349
039s_E14


title: kidney cell 350, Lean, 20 weeks

description:
kidney cell 350
039s_E15


title: kidney cell 345, Lean, 20 weeks

description:
kidney cell 345
039s_E10


title: kidney cell 346, Lean, 20 weeks

description:
kidney cell 346
039s_E11


title: kidney cell 344, Lean, 20 weeks

description:
kidney cell 344
039s_E1


title: MGH170-P9-E07-CD45neg, Smart-seq2


title: MGH170-P9-C12-CD45neg, Smart-seq2


title: kidney cell 342, Lean, 20 weeks

description:
kidney cell 342
039s_D7


title: MGH170-P9-C08-CD45neg, Smart-seq2


title: kidney cell 347, Lean, 20 weeks

description:
kidney cell 347
039s_E12


title: MGH170-P9-C07-CD45neg, Smart-seq2


title: MGH170-P9-C02-CD45neg, Smart-seq2


title: MGH170-P9-C05-CD45neg, Smart-seq2


title: MGH170-P9-C06-CD45neg, Smart-seq2


title: kidney cell 340, Lean, 20 weeks

description:
kidney cell 340
039s_D21


title: kidney cell 341, Lean, 20 weeks

description:
kidney cell 341
039s_D4


title: kidney cell 343, Lean, 20 weeks

description:
kidney cell 343
039s_D9


title: kidney cell 337, Lean, 20 weeks

description:
kidney cell 337
039s_D18


title: MGH170-P9-B10-CD45neg, Smart-seq2


title: MGH170-P9-B03-CD45neg, Smart-seq2


title: MGH170-P9-B01-CD45neg, Smart-seq2


title: MGH170-P9-B09-CD45neg, Smart-seq2


title: kidney cell 335, Lean, 20 weeks

description:
kidney cell 335
039s_D15


title: MGH170-P9-B04-CD45neg, Smart-seq2


title: MGH170-P9-B08-CD45neg, Smart-seq2


title: kidney cell 339, Lean, 20 weeks

description:
kidney cell 339
039s_D20


title: kidney cell 348, Lean, 20 weeks

description:
kidney cell 348
039s_E13


title: kidney cell 334, Lean, 20 weeks

description:
kidney cell 334
039s_D14


title: kidney cell 336, Lean, 20 weeks

description:
kidney cell 336
039s_D16


title: MGH170-P9-B12-CD45neg, Smart-seq2


title: MGH170-P9-A10-CD45neg, Smart-seq2


title: kidney cell 338, Lean, 20 weeks

description:
kidney cell 338
039s_D19


title: MGH170-P9-A09-CD45neg, Smart-seq2


title: MGH170-P9-A05-CD45neg, Smart-seq2


title: kidney cell 331, Lean, 20 weeks

description:
kidney cell 331
039s_C7


title: MGH170-P9-B05-CD45neg, Smart-seq2


title: kidney cell 332, Lean, 20 weeks

description:
kidney cell 332
039s_C8


title: MGH170-P9-A06-CD45neg, Smart-seq2


title: kidney cell 333, Lean, 20 weeks

description:
kidney cell 333
039s_C9


title: MGH170-P9-A04-CD45neg, Smart-seq2


title: MGH170-P9-A01-CD45neg, Smart-seq2


title: kidney cell 328, Lean, 20 weeks

description:
kidney cell 328
039s_C4


title: MGH170-P6-H06-CD45neg, Smart-seq2


title: kidney cell 330, Lean, 20 weeks

description:
kidney cell 330
039s_C6


title: MGH170-P6-H04-CD45neg, Smart-seq2


title: kidney cell 329, Lean, 20 weeks

description:
kidney cell 329
039s_C5


title: kidney cell 326, Lean, 20 weeks

description:
kidney cell 326
039s_C24


title: kidney cell 327, Lean, 20 weeks

description:
kidney cell 327
039s_C3


title: MGH170-P6-H01-CD45neg, Smart-seq2


title: MGH170-P6-H02-CD45neg, Smart-seq2


title: kidney cell 324, Lean, 20 weeks

description:
kidney cell 324
039s_C22


title: kidney cell 325, Lean, 20 weeks

description:
kidney cell 325
039s_C23


title: MGH170-P6-G10-CD45neg, Smart-seq2


title: kidney cell 322, Lean, 20 weeks

description:
kidney cell 322
039s_C20


title: kidney cell 323, Lean, 20 weeks

description:
kidney cell 323
039s_C21


title: MGH170-P6-G12-CD45neg, Smart-seq2


title: kidney cell 320, Lean, 20 weeks

description:
kidney cell 320
039s_C19


title: kidney cell 321, Lean, 20 weeks

description:
kidney cell 321
039s_C2


title: MGH170-P6-G03-CD45neg, Smart-seq2


title: MGH170-P6-G09-CD45neg, Smart-seq2


title: MGH170-P6-G01-CD45neg, Smart-seq2


title: kidney cell 318, Lean, 20 weeks

description:
kidney cell 318
039s_C16


title: MGH170-P6-F08-CD45neg, Smart-seq2


title: MGH170-P6-F06-CD45neg, Smart-seq2


title: kidney cell 316, Lean, 20 weeks

description:
kidney cell 316
039s_C13


title: kidney cell 315, Lean, 20 weeks

description:
kidney cell 315
039s_C12


title: kidney cell 317, Lean, 20 weeks

description:
kidney cell 317
039s_C14


title: MGH170-P6-F03-CD45neg, Smart-seq2


title: MGH170-P6-F04-CD45neg, Smart-seq2


title: kidney cell 314, Lean, 20 weeks

description:
kidney cell 314
039s_C11


title: kidney cell 313, Lean, 20 weeks

description:
kidney cell 313
039s_C1


title: MGH170-P6-F02-CD45neg, Smart-seq2


title: MGH170-P6-G11-CD45neg, Smart-seq2


title: kidney cell 311, Lean, 20 weeks

description:
kidney cell 311
039s_B8


title: kidney cell 312, Lean, 20 weeks

description:
kidney cell 312
039s_B9


title: MGH170-P6-G07-CD45neg, Smart-seq2


title: MGH170-P6-E12-CD45neg, Smart-seq2


title: MGH170-P6-E09-CD45neg, Smart-seq2


title: kidney cell 310, Lean, 20 weeks

description:
kidney cell 310
039s_B7


title: kidney cell 309, Lean, 20 weeks

description:
kidney cell 309
039s_B6


title: MGH170-P6-E04-CD45neg, Smart-seq2


title: kidney cell 319, Lean, 20 weeks

description:
kidney cell 319
039s_C17


title: kidney cell 308, Lean, 20 weeks

description:
kidney cell 308
039s_B5


title: MGH170-P6-E01-CD45neg, Smart-seq2


title: MGH170-P6-E06-CD45neg, Smart-seq2


title: MGH170-P6-D10-CD45neg, Smart-seq2


title: kidney cell 307, Lean, 20 weeks

description:
kidney cell 307
039s_B4


title: kidney cell 305, Lean, 20 weeks

description:
kidney cell 305
039s_B24


title: MGH170-P6-D09-CD45neg, Smart-seq2


title: kidney cell 303, Lean, 20 weeks

description:
kidney cell 303
039s_B20


title: MGH170-P6-D05-CD45neg, Smart-seq2


title: MGH170-P6-F01-CD45neg, Smart-seq2


title: kidney cell 302, Lean, 20 weeks

description:
kidney cell 302
039s_B2


title: kidney cell 304, Lean, 20 weeks

description:
kidney cell 304
039s_B22


title: MGH170-P6-D03-CD45neg, Smart-seq2


title: kidney cell 299, Lean, 20 weeks

description:
kidney cell 299
039s_B17


title: kidney cell 301, Lean, 20 weeks

description:
kidney cell 301
039s_B19


title: MGH170-P6-D01-CD45neg, Smart-seq2


title: MGH170-P6-D08-CD45neg, Smart-seq2


title: kidney cell 306, Lean, 20 weeks

description:
kidney cell 306
039s_B3


title: MGH170-P6-C09-CD45neg, Smart-seq2


title: kidney cell 296, Lean, 20 weeks

description:
kidney cell 296
039s_B13


title: MGH170-P6-C05-CD45neg, Smart-seq2


title: kidney cell 295, Lean, 20 weeks

description:
kidney cell 295
039s_B12


title: MGH170-P6-B12-CD45neg, Smart-seq2


title: MGH170-P6-D02-CD45neg, Smart-seq2


title: MGH170-P6-B09-CD45neg, Smart-seq2


title: kidney cell 292, Lean, 20 weeks

description:
kidney cell 292
039s_A9


title: MGH170-P6-C11-CD45neg, Smart-seq2


title: MGH170-P6-B10-CD45neg, Smart-seq2


title: kidney cell 297, Lean, 20 weeks

description:
kidney cell 297
039s_B14


title: kidney cell 293, Lean, 20 weeks

description:
kidney cell 293
039s_B1


title: MGH170-P6-B07-CD45neg, Smart-seq2


title: MGH170-P6-C02-CD45neg, Smart-seq2


title: kidney cell 291, Lean, 20 weeks

description:
kidney cell 291
039s_A8


title: kidney cell 300, Lean, 20 weeks

description:
kidney cell 300
039s_B18


title: kidney cell 290, Lean, 20 weeks

description:
kidney cell 290
039s_A7


title: MGH170-P6-B06-CD45neg, Smart-seq2


title: MGH170-P6-B03-CD45neg, Smart-seq2


title: kidney cell 294, Lean, 20 weeks

description:
kidney cell 294
039s_B11


title: kidney cell 289, Lean, 20 weeks

description:
kidney cell 289
039s_A6


title: kidney cell 288, Lean, 20 weeks

description:
kidney cell 288
039s_A5


title: kidney cell 298, Lean, 20 weeks

description:
kidney cell 298
039s_B15


title: MGH170-P6-C04-CD45neg, Smart-seq2


title: MGH170-P6-A10-CD45neg, Smart-seq2


title: kidney cell 285, Lean, 20 weeks

description:
kidney cell 285
039s_A23


title: MGH170-P6-A06-CD45neg, Smart-seq2


title: MGH170-P6-B01-CD45neg, Smart-seq2


title: kidney cell 287, Lean, 20 weeks

description:
kidney cell 287
039s_A4


title: MGH170-P6-A03-CD45neg, Smart-seq2


title: kidney cell 283, Lean, 20 weeks

description:
kidney cell 283
039s_A21


title: MGH170-P1-H11-CD45neg, Smart-seq2


title: kidney cell 284, Lean, 20 weeks

description:
kidney cell 284
039s_A22


title: MGH170-P1-H08-CD45neg, Smart-seq2


title: MGH170-P1-H05-CD45neg, Smart-seq2


title: MGH170-P1-H01-CD45neg, Smart-seq2


title: MGH170-P6-B04-CD45neg, Smart-seq2


title: kidney cell 280, Lean, 20 weeks

description:
kidney cell 280
039s_A19


title: kidney cell 278, Lean, 20 weeks

description:
kidney cell 278
039s_A17


title: kidney cell 279, Lean, 20 weeks

description:
kidney cell 279
039s_A18


title: MGH170-P1-G10-CD45neg, Smart-seq2


title: kidney cell 286, Lean, 20 weeks

description:
kidney cell 286
039s_A3


title: MGH170-P1-G09-CD45neg, Smart-seq2


title: MGH170-P1-G08-CD45neg, Smart-seq2


title: MGH170-P6-A02-CD45neg, Smart-seq2


title: kidney cell 277, Lean, 20 weeks

description:
kidney cell 277
039s_A16


title: MGH170-P1-G05-CD45neg, Smart-seq2


title: kidney cell 281, Lean, 20 weeks

description:
kidney cell 281
039s_A2


title: kidney cell 282, Lean, 20 weeks

description:
kidney cell 282
039s_A20


title: MGH170-P1-G03-CD45neg, Smart-seq2


title: kidney cell 275, Lean, 20 weeks

description:
kidney cell 275
039s_A14


title: MGH170-P1-G06-CD45neg, Smart-seq2


title: kidney cell 271, Lean, 20 weeks

description:
kidney cell 271
039s_A10


title: kidney cell 270, Lean, 20 weeks

description:
kidney cell 270
039s_A1


title: kidney cell 273, Lean, 20 weeks

description:
kidney cell 273
039s_A12


title: MGH170-P1-G02-CD45neg, Smart-seq2


title: kidney cell 272, Lean, 20 weeks

description:
kidney cell 272
039s_A11


title: MGH170-P1-F10-CD45neg, Smart-seq2


title: kidney cell 274, Lean, 20 weeks

description:
kidney cell 274
039s_A13


title: MGH170-P1-F09-CD45neg, Smart-seq2


title: kidney cell 269, Lean, 20 weeks

description:
kidney cell 269
038s_P9


title: kidney cell 276, Lean, 20 weeks

description:
kidney cell 276
039s_A15


title: kidney cell 268, Lean, 20 weeks

description:
kidney cell 268
038s_P8


title: MGH170-P1-F07-CD45neg, Smart-seq2


title: MGH170-P1-F08-CD45neg, Smart-seq2


title: kidney cell 266, Lean, 20 weeks

description:
kidney cell 266
038s_P5


title: MGH170-P1-F02-CD45neg, Smart-seq2


title: MGH170-P1-F04-CD45neg, Smart-seq2


title: kidney cell 264, Lean, 20 weeks

description:
kidney cell 264
038s_P3


title: MGH170-P1-G01-CD45neg, Smart-seq2


title: kidney cell 265, Lean, 20 weeks

description:
kidney cell 265
038s_P4


title: MGH170-P1-F01-CD45neg, Smart-seq2


title: kidney cell 263, Lean, 20 weeks

description:
kidney cell 263
038s_P22


title: kidney cell 261, Lean, 20 weeks

description:
kidney cell 261
038s_P2


title: MGH170-P1-E12-CD45neg, Smart-seq2


title: MGH170-P1-E08-CD45neg, Smart-seq2


title: kidney cell 262, Lean, 20 weeks

description:
kidney cell 262
038s_P21


title: MGH170-P1-E05-CD45neg, Smart-seq2


title: kidney cell 267, Lean, 20 weeks

description:
kidney cell 267
038s_P7


title: kidney cell 260, Lean, 20 weeks

description:
kidney cell 260
038s_P19


title: MGH170-P1-E04-CD45neg, Smart-seq2


title: kidney cell 259, Lean, 20 weeks

description:
kidney cell 259
038s_P18


title: MGH170-P1-D11-CD45neg, Smart-seq2


title: MGH170-P1-D12-CD45neg, Smart-seq2


title: kidney cell 257, Lean, 20 weeks

description:
kidney cell 257
038s_P16


title: MGH170-P1-D09-CD45neg, Smart-seq2


title: kidney cell 258, Lean, 20 weeks

description:
kidney cell 258
038s_P17


title: kidney cell 256, Lean, 20 weeks

description:
kidney cell 256
038s_P15


title: MGH170-P1-D05-CD45neg, Smart-seq2


title: MGH170-P1-D08-CD45neg, Smart-seq2


title: MGH170-P1-D07-CD45neg, Smart-seq2


title: kidney cell 255, Lean, 20 weeks

description:
kidney cell 255
038s_P14


title: kidney cell 254, Lean, 20 weeks

description:
kidney cell 254
038s_P13


title: kidney cell 253, Lean, 20 weeks

description:
kidney cell 253
038s_P12


title: MGH170-P1-D04-CD45neg, Smart-seq2


title: kidney cell 252, Lean, 20 weeks

description:
kidney cell 252
038s_P11


title: MGH170-P1-C11-CD45neg, Smart-seq2


title: MGH170-P1-C10-CD45neg, Smart-seq2


title: kidney cell 251, Lean, 20 weeks

description:
kidney cell 251
038s_P10


title: kidney cell 248, Lean, 20 weeks

description:
kidney cell 248
038s_O6


title: kidney cell 247, Lean, 20 weeks

description:
kidney cell 247
038s_O5


title: MGH170-P1-C12-CD45neg, Smart-seq2


title: MGH170-P1-E01-CD45neg, Smart-seq2


title: kidney cell 250, Lean, 20 weeks

description:
kidney cell 250
038s_O9


title: MGH170-P1-C07-CD45neg, Smart-seq2


title: MGH170-P1-C09-CD45neg, Smart-seq2


title: kidney cell 246, Lean, 20 weeks

description:
kidney cell 246
038s_O4


title: kidney cell 244, Lean, 20 weeks

description:
kidney cell 244
038s_O23


title: MGH170-P1-C01-CD45neg, Smart-seq2


title: kidney cell 243, Lean, 20 weeks

description:
kidney cell 243
038s_O22


title: MGH170-P1-B09-CD45neg, Smart-seq2


title: kidney cell 249, Lean, 20 weeks

description:
kidney cell 249
038s_O7


title: kidney cell 245, Lean, 20 weeks

description:
kidney cell 245
038s_O3


title: kidney cell 241, Lean, 20 weeks

description:
kidney cell 241
038s_O19


title: MGH170-P1-B06-CD45neg, Smart-seq2


title: MGH170-P1-B08-CD45neg, Smart-seq2


title: MGH170-P1-C05-CD45neg, Smart-seq2


title: kidney cell 239, Lean, 20 weeks

description:
kidney cell 239
038s_O16


title: MGH170-P1-C02-CD45neg, Smart-seq2


title: kidney cell 238, Lean, 20 weeks

description:
kidney cell 238
038s_O15


title: kidney cell 240, Lean, 20 weeks

description:
kidney cell 240
038s_O17


title: MGH170-P1-B10-CD45neg, Smart-seq2


title: MGH170-P1-B07-CD45neg, Smart-seq2


title: kidney cell 242, Lean, 20 weeks

description:
kidney cell 242
038s_O21


title: kidney cell 233, Lean, 20 weeks

description:
kidney cell 233
038s_O10


title: MGH170-P1-B04-CD45neg, Smart-seq2


title: MGH170-P1-A12-CD45neg, Smart-seq2


title: kidney cell 232, Lean, 20 weeks

description:
kidney cell 232
038s_N23


title: MGH170-P1-B03-CD45neg, Smart-seq2


title: kidney cell 236, Lean, 20 weeks

description:
kidney cell 236
038s_O13


title: MGH170-P1-B05-CD45neg, Smart-seq2


title: MGH170-P1-C06-CD45neg, Smart-seq2


title: MGH170-P1-A09-CD45neg, Smart-seq2


title: kidney cell 231, Lean, 20 weeks

description:
kidney cell 231
038s_N21


title: kidney cell 237, Lean, 20 weeks

description:
kidney cell 237
038s_O14


title: kidney cell 234, Lean, 20 weeks

description:
kidney cell 234
038s_O11


title: MGH170-P1-B02-CD45neg, Smart-seq2


title: kidney cell 235, Lean, 20 weeks

description:
kidney cell 235
038s_O12


title: kidney cell 230, Lean, 20 weeks

description:
kidney cell 230
038s_N19


title: kidney cell 229, Lean, 20 weeks

description:
kidney cell 229
038s_N18


title: MGH170-P1-A06-CD45neg, Smart-seq2


title: MGH170-P1-A07-CD45neg, Smart-seq2


title: MGH170-P8-H12-CD45pos, Smart-seq2

source_name: Oligodendroglioma single cell, MGH170-CD45pos


title: kidney cell 227, Lean, 20 weeks

description:
kidney cell 227
038s_N16


title: MGH170-P1-A04-CD45neg, Smart-seq2


title: kidney cell 225, Lean, 20 weeks

description:
kidney cell 225
038s_N11


title: kidney cell 226, Lean, 20 weeks

description:
kidney cell 226
038s_N15


title: MGH170-P8-H11-CD45pos, Smart-seq2

value: Oligodendroglioma single cell, MGH170-CD45pos


title: MGH170-P8-H10-CD45pos, Smart-seq2


title: MGH170-P8-H08-CD45pos, Smart-seq2


title: MGH170-P8-H07-CD45pos, Smart-seq2


title: MGH170-P8-H06-CD45pos, Smart-seq2


title: kidney cell 222, Lean, 20 weeks

description:
kidney cell 222
038s_M9


title: kidney cell 221, Lean, 20 weeks

description:
kidney cell 221
038s_M8


title: MGH170-P8-H05-CD45pos, Smart-seq2


title: MGH170-P8-H04-CD45pos, Smart-seq2


title: kidney cell 219, Lean, 20 weeks

description:
kidney cell 219
038s_M6


title: kidney cell 218, Lean, 20 weeks

description:
kidney cell 218
038s_M5


title: kidney cell 220, Lean, 20 weeks

description:
kidney cell 220
038s_M7


title: MGH170-P8-H01-CD45pos, Smart-seq2


title: kidney cell 217, Lean, 20 weeks

description:
kidney cell 217
038s_M4


title: kidney cell 228, Lean, 20 weeks

description:
kidney cell 228
038s_N17


title: MGH170-P1-A05-CD45neg, Smart-seq2


title: kidney cell 216, Lean, 20 weeks

description:
kidney cell 216
038s_M3


title: MGH170-P8-G11-CD45pos, Smart-seq2


title: MGH170-P8-G10-CD45pos, Smart-seq2


title: MGH170-P8-G12-CD45pos, Smart-seq2


title: MGH170-P1-A10-CD45neg, Smart-seq2


title: MGH170-P8-G09-CD45pos, Smart-seq2


title: MGH170-P8-G08-CD45pos, Smart-seq2


title: kidney cell 213, Lean, 20 weeks

description:
kidney cell 213
038s_M21


title: kidney cell 215, Lean, 20 weeks

description:
kidney cell 215
038s_M23


title: kidney cell 224, Lean, 20 weeks

description:
kidney cell 224
038s_N10


title: kidney cell 212, Lean, 20 weeks

description:
kidney cell 212
038s_M2


title: kidney cell 214, Lean, 20 weeks

description:
kidney cell 214
038s_M22


title: MGH170-P8-G07-CD45pos, Smart-seq2


title: kidney cell 211, Lean, 20 weeks

description:
kidney cell 211
038s_M18


title: MGH170-P8-G04-CD45pos, Smart-seq2


title: kidney cell 223, Lean, 20 weeks

description:
kidney cell 223
038s_N1


title: MGH170-P8-G03-CD45pos, Smart-seq2


title: MGH170-P8-G02-CD45pos, Smart-seq2


title: kidney cell 210, Lean, 20 weeks

description:
kidney cell 210
038s_M17


title: kidney cell 209, Lean, 20 weeks

description:
kidney cell 209
038s_M16


title: MGH170-P8-F11-CD45pos, Smart-seq2


title: MGH170-P8-F12-CD45pos, Smart-seq2


title: kidney cell 208, Lean, 20 weeks

description:
kidney cell 208
038s_M15


title: MGH170-P8-F09-CD45pos, Smart-seq2


title: MGH170-P8-F10-CD45pos, Smart-seq2


title: kidney cell 206, Lean, 20 weeks

description:
kidney cell 206
038s_M13


title: kidney cell 205, Lean, 20 weeks

description:
kidney cell 205
038s_M12


title: kidney cell 204, Lean, 20 weeks

description:
kidney cell 204
038s_M11


title: kidney cell 202, Lean, 20 weeks

description:
kidney cell 202
038s_M1


title: MGH170-P8-F05-CD45pos, Smart-seq2


title: MGH170-P8-F07-CD45pos, Smart-seq2


title: kidney cell 203, Lean, 20 weeks

description:
kidney cell 203
038s_M10


title: MGH170-P8-F04-CD45pos, Smart-seq2


title: MGH170-P8-F06-CD45pos, Smart-seq2


title: MGH170-P8-F02-CD45pos, Smart-seq2


title: MGH170-P8-F01-CD45pos, Smart-seq2


title: kidney cell 201, Lean, 20 weeks

description:
kidney cell 201
038s_K9


title: kidney cell 199, Lean, 20 weeks

description:
kidney cell 199
038s_K4


title: kidney cell 198, Lean, 20 weeks

description:
kidney cell 198
038s_K3


title: MGH170-P8-E11-CD45pos, Smart-seq2


title: kidney cell 196, Lean, 20 weeks

description:
kidney cell 196
038s_K22


title: kidney cell 200, Lean, 20 weeks

description:
kidney cell 200
038s_K7


title: kidney cell 195, Lean, 20 weeks

description:
kidney cell 195
038s_K21


title: MGH170-P8-E09-CD45pos, Smart-seq2


title: MGH170-P8-E05-CD45pos, Smart-seq2


title: kidney cell 207, Lean, 20 weeks

description:
kidney cell 207
038s_M14


title: kidney cell 194, Lean, 20 weeks

description:
kidney cell 194
038s_K2


title: MGH170-P8-E04-CD45pos, Smart-seq2


title: kidney cell 193, Lean, 20 weeks

description:
kidney cell 193
038s_K19


title: MGH170-P8-E01-CD45pos, Smart-seq2


title: MGH170-P8-E03-CD45pos, Smart-seq2


title: kidney cell 191, Lean, 20 weeks

description:
kidney cell 191
038s_K17


title: kidney cell 192, Lean, 20 weeks

description:
kidney cell 192
038s_K18


title: MGH170-P8-D12-CD45pos, Smart-seq2


title: kidney cell 190, Lean, 20 weeks

description:
kidney cell 190
038s_K15


title: MGH170-P8-D11-CD45pos, Smart-seq2


title: kidney cell 197, Lean, 20 weeks

description:
kidney cell 197
038s_K23


title: MGH170-P8-D10-CD45pos, Smart-seq2


title: kidney cell 188, Lean, 20 weeks

description:
kidney cell 188
038s_K13


title: MGH170-P8-D08-CD45pos, Smart-seq2


title: MGH170-P8-E10-CD45pos, Smart-seq2


title: MGH170-P8-D05-CD45pos, Smart-seq2


title: kidney cell 187, Lean, 20 weeks

description:
kidney cell 187
038s_K12


title: kidney cell 186, Lean, 20 weeks

description:
kidney cell 186
038s_K11


title: MGH170-P8-D07-CD45pos, Smart-seq2


title: kidney cell 184, Lean, 20 weeks

description:
kidney cell 184
038s_K1


title: kidney cell 183, Lean, 20 weeks

description:
kidney cell 183
038s_J9


title: MGH170-P8-D04-CD45pos, Smart-seq2


title: MGH170-P8-D03-CD45pos, Smart-seq2


title: kidney cell 185, Lean, 20 weeks

description:
kidney cell 185
038s_K10


title: MGH170-P8-E08-CD45pos, Smart-seq2


title: kidney cell 181, Lean, 20 weeks

description:
kidney cell 181
038s_J6


title: kidney cell 182, Lean, 20 weeks

description:
kidney cell 182
038s_J7


title: MGH170-P8-C11-CD45pos, Smart-seq2


title: MGH170-P8-D02-CD45pos, Smart-seq2


title: kidney cell 179, Lean, 20 weeks

description:
kidney cell 179
038s_J4


title: kidney cell 180, Lean, 20 weeks

description:
kidney cell 180
038s_J5


title: MGH170-P8-C09-CD45pos, Smart-seq2


title: MGH170-P8-C07-CD45pos, Smart-seq2


title: kidney cell 178, Lean, 20 weeks

description:
kidney cell 178
038s_J3


title: kidney cell 177, Lean, 20 weeks

description:
kidney cell 177
038s_J23


title: MGH170-P8-C06-CD45pos, Smart-seq2


title: kidney cell 175, Lean, 20 weeks

description:
kidney cell 175
038s_J21


title: MGH170-P8-C04-CD45pos, Smart-seq2


title: kidney cell 189, Lean, 20 weeks

description:
kidney cell 189
038s_K14


title: kidney cell 174, Lean, 20 weeks

description:
kidney cell 174
038s_J2


title: kidney cell 173, Lean, 20 weeks

description:
kidney cell 173
038s_J19


title: MGH170-P8-C01-CD45pos, Smart-seq2


title: MGH170-P8-B12-CD45pos, Smart-seq2


title: MGH170-P8-C05-CD45pos, Smart-seq2


title: MGH170-P8-B10-CD45pos, Smart-seq2


title: kidney cell 171, Lean, 20 weeks

description:
kidney cell 171
038s_J17


title: kidney cell 170, Lean, 20 weeks

description:
kidney cell 170
038s_J16


title: MGH170-P8-C03-CD45pos, Smart-seq2


title: kidney cell 168, Lean, 20 weeks

description:
kidney cell 168
038s_J14


title: MGH170-P8-B09-CD45pos, Smart-seq2


title: kidney cell 172, Lean, 20 weeks

description:
kidney cell 172
038s_J18


title: MGH170-P8-C10-CD45pos, Smart-seq2


title: MGH170-P8-B08-CD45pos, Smart-seq2


title: kidney cell 167, Lean, 20 weeks

description:
kidney cell 167
038s_J13


title: kidney cell 166, Lean, 20 weeks

description:
kidney cell 166
038s_J12


title: kidney cell 169, Lean, 20 weeks

description:
kidney cell 169
038s_J15


title: MGH170-P8-B06-CD45pos, Smart-seq2


title: MGH170-P8-B07-CD45pos, Smart-seq2


title: MGH170-P8-B03-CD45pos, Smart-seq2


title: MGH170-P8-C08-CD45pos, Smart-seq2


title: MGH170-P8-B05-CD45pos, Smart-seq2


title: kidney cell 164, Lean, 20 weeks

description:
kidney cell 164
038s_J10


title: kidney cell 165, Lean, 20 weeks

description:
kidney cell 165
038s_J11


title: kidney cell 176, Lean, 20 weeks

description:
kidney cell 176
038s_J22


title: kidney cell 163, Lean, 20 weeks

description:
kidney cell 163
038s_J1


title: MGH170-P8-B02-CD45pos, Smart-seq2


title: MGH170-P8-B01-CD45pos, Smart-seq2


title: kidney cell 161, Lean, 20 weeks

description:
kidney cell 161
038s_I7


title: kidney cell 160, Lean, 20 weeks

description:
kidney cell 160
038s_I5


title: kidney cell 162, Lean, 20 weeks

description:
kidney cell 162
038s_I9


title: kidney cell 159, Lean, 20 weeks

description:
kidney cell 159
038s_I4


title: MGH170-P8-A11-CD45pos, Smart-seq2


title: MGH170-P8-A09-CD45pos, Smart-seq2


title: MGH170-P8-A05-CD45pos, Smart-seq2


title: kidney cell 157, Lean, 20 weeks

description:
kidney cell 157
038s_I23


title: MGH170-P8-A06-CD45pos, Smart-seq2


title: kidney cell 156, Lean, 20 weeks

description:
kidney cell 156
038s_I22


title: kidney cell 155, Lean, 20 weeks

description:
kidney cell 155
038s_I2


title: MGH170-P8-A07-CD45pos, Smart-seq2


title: MGH170-P8-A04-CD45pos, Smart-seq2


title: MGH170-P8-A03-CD45pos, Smart-seq2


title: MGH170-P8-A01-CD45pos, Smart-seq2


title: kidney cell 153, Lean, 20 weeks

description:
kidney cell 153
038s_I18


title: kidney cell 152, Lean, 20 weeks

description:
kidney cell 152
038s_I17


title: MGH170-P7-H12-CD45pos, Smart-seq2


title: kidney cell 154, Lean, 20 weeks

description:
kidney cell 154
038s_I19


title: MGH170-P7-H11-CD45pos, Smart-seq2


title: MGH170-P7-H10-CD45pos, Smart-seq2


title: MGH170-P7-H09-CD45pos, Smart-seq2


title: kidney cell 158, Lean, 20 weeks

description:
kidney cell 158
038s_I3


title: MGH170-P7-H07-CD45pos, Smart-seq2


title: kidney cell 148, Lean, 20 weeks

description:
kidney cell 148
038s_I12


title: kidney cell 149, Lean, 20 weeks

description:
kidney cell 149
038s_I13


title: MGH170-P8-A10-CD45pos, Smart-seq2


title: kidney cell 147, Lean, 20 weeks

description:
kidney cell 147
038s_I11


title: MGH170-P7-H08-CD45pos, Smart-seq2


title: kidney cell 151, Lean, 20 weeks

description:
kidney cell 151
038s_I16


title: MGH170-P7-H03-CD45pos, Smart-seq2


title: MGH170-P7-H04-CD45pos, Smart-seq2


title: MGH170-P7-G12-CD45pos, Smart-seq2


title: kidney cell 146, Lean, 20 weeks

description:
kidney cell 146
038s_I10


title: kidney cell 145, Lean, 20 weeks

description:
kidney cell 145
038s_I1


title: kidney cell 142, Lean, 20 weeks

description:
kidney cell 142
038s_H5


title: MGH170-P7-G11-CD45pos, Smart-seq2


title: kidney cell 143, Lean, 20 weeks

description:
kidney cell 143
038s_H6


title: kidney cell 144, Lean, 20 weeks

description:
kidney cell 144
038s_H7


title: kidney cell 141, Lean, 20 weeks

description:
kidney cell 141
038s_H4


title: MGH170-P7-G09-CD45pos, Smart-seq2


title: kidney cell 150, Lean, 20 weeks

description:
kidney cell 150
038s_I15


title: MGH170-P7-G07-CD45pos, Smart-seq2


title: kidney cell 139, Lean, 20 weeks

description:
kidney cell 139
038s_H23


title: kidney cell 138, Lean, 20 weeks

description:
kidney cell 138
038s_H22


title: MGH170-P7-G05-CD45pos, Smart-seq2


title: kidney cell 137, Lean, 20 weeks

description:
kidney cell 137
038s_H21


title: kidney cell 136, Lean, 20 weeks

description:
kidney cell 136
038s_H2


title: MGH170-P7-G03-CD45pos, Smart-seq2


title: MGH170-P7-G04-CD45pos, Smart-seq2


title: MGH170-P7-G10-CD45pos, Smart-seq2


title: kidney cell 135, Lean, 20 weeks

description:
kidney cell 135
038s_H19


title: MGH170-P7-G02-CD45pos, Smart-seq2


title: kidney cell 134, Lean, 20 weeks

description:
kidney cell 134
038s_H17


title: kidney cell 132, Lean, 20 weeks

description:
kidney cell 132
038s_H15


title: MGH170-P7-G01-CD45pos, Smart-seq2


title: MGH170-P7-F10-CD45pos, Smart-seq2


title: kidney cell 131, Lean, 20 weeks

description:
kidney cell 131
038s_H14


title: MGH170-P7-G08-CD45pos, Smart-seq2


title: MGH170-P7-F09-CD45pos, Smart-seq2


title: kidney cell 130, Lean, 20 weeks

description:
kidney cell 130
038s_H13


title: kidney cell 140, Lean, 20 weeks

description:
kidney cell 140
038s_H3


title: MGH170-P7-F05-CD45pos, Smart-seq2


title: kidney cell 128, Lean, 20 weeks

description:
kidney cell 128
038s_H10


title: MGH170-P7-F06-CD45pos, Smart-seq2


title: MGH170-P7-F03-CD45pos, Smart-seq2


title: kidney cell 126, Lean, 20 weeks

description:
kidney cell 126
038s_G9


title: MGH170-P7-F02-CD45pos, Smart-seq2


title: MGH170-P7-F04-CD45pos, Smart-seq2


title: kidney cell 127, Lean, 20 weeks

description:
kidney cell 127
038s_H1


title: kidney cell 124, Lean, 20 weeks

description:
kidney cell 124
038s_G6


title: MGH170-P7-G06-CD45pos, Smart-seq2


title: kidney cell 125, Lean, 20 weeks

description:
kidney cell 125
038s_G7


title: kidney cell 133, Lean, 20 weeks

description:
kidney cell 133
038s_H16


title: kidney cell 123, Lean, 20 weeks

description:
kidney cell 123
038s_G5


title: MGH170-P7-E10-CD45pos, Smart-seq2


title: kidney cell 122, Lean, 20 weeks

description:
kidney cell 122
038s_G4


title: MGH170-P7-E06-CD45pos, Smart-seq2


title: kidney cell 121, Lean, 20 weeks

description:
kidney cell 121
038s_G23


title: MGH170-P7-F01-CD45pos, Smart-seq2


title: MGH170-P7-F07-CD45pos, Smart-seq2


title: kidney cell 120, Lean, 20 weeks

description:
kidney cell 120
038s_G22


title: MGH170-P7-E03-CD45pos, Smart-seq2


title: kidney cell 119, Lean, 20 weeks

description:
kidney cell 119
038s_G21


title: MGH170-P7-E02-CD45pos, Smart-seq2


title: kidney cell 117, Lean, 20 weeks

description:
kidney cell 117
038s_G19


title: MGH170-P7-E01-CD45pos, Smart-seq2


title: kidney cell 129, Lean, 20 weeks

description:
kidney cell 129
038s_H11


title: kidney cell 118, Lean, 20 weeks

description:
kidney cell 118
038s_G2


title: MGH170-P7-D10-CD45pos, Smart-seq2


title: kidney cell 114, Lean, 20 weeks

description:
kidney cell 114
038s_G16


title: MGH170-P7-D09-CD45pos, Smart-seq2


title: MGH170-P7-D08-CD45pos, Smart-seq2


title: MGH170-P7-E11-CD45pos, Smart-seq2


title: kidney cell 112, Lean, 20 weeks

description:
kidney cell 112
038s_G14


title: MGH170-P7-D06-CD45pos, Smart-seq2


title: MGH170-P7-D05-CD45pos, Smart-seq2


title: kidney cell 113, Lean, 20 weeks

description:
kidney cell 113
038s_G15


title: MGH170-P7-D04-CD45pos, Smart-seq2


title: kidney cell 108, Lean, 20 weeks

description:
kidney cell 108
038s_G1


title: MGH170-P7-D02-CD45pos, Smart-seq2


title: MGH170-P7-D01-CD45pos, Smart-seq2


title: kidney cell 111, Lean, 20 weeks

description:
kidney cell 111
038s_G13


title: MGH170-P7-E05-CD45pos, Smart-seq2


title: MGH170-P7-C12-CD45pos, Smart-seq2


title: kidney cell 109, Lean, 20 weeks

description:
kidney cell 109
038s_G11


title: kidney cell 110, Lean, 20 weeks

description:
kidney cell 110
038s_G12


title: MGH170-P7-C11-CD45pos, Smart-seq2


title: kidney cell 107, Lean, 20 weeks

description:
kidney cell 107
038s_F9


title: MGH170-P7-C07-CD45pos, Smart-seq2


title: MGH170-P7-C05-CD45pos, Smart-seq2


title: kidney cell 116, Lean, 20 weeks

description:
kidney cell 116
038s_G18


title: MGH170-P7-D12-CD45pos, Smart-seq2


title: kidney cell 103, Lean, 20 weeks

description:
kidney cell 103
038s_F4


title: kidney cell 115, Lean, 20 weeks

description:
kidney cell 115
038s_G17


title: MGH170-P7-B10-CD45pos, Smart-seq2


title: kidney cell 102, Lean, 20 weeks

description:
kidney cell 102
038s_F3


title: MGH170-P7-B08-CD45pos, Smart-seq2


title: kidney cell 101, Lean, 20 weeks

description:
kidney cell 101
038s_F23


title: MGH170-P7-B06-CD45pos, Smart-seq2


title: kidney cell 100, Lean, 20 weeks

description:
kidney cell 100
038s_F22


title: MGH170-P7-B05-CD45pos, Smart-seq2


title: kidney cell 99, Lean, 20 weeks

description:
kidney cell 99
038s_F21


title: MGH170-P7-B03-CD45pos, Smart-seq2


title: kidney cell 105, Lean, 20 weeks

description:
kidney cell 105
038s_F6


title: kidney cell 98, Lean, 20 weeks

description:
kidney cell 98
038s_F20


title: kidney cell 97, Lean, 20 weeks

description:
kidney cell 97
038s_F2


title: kidney cell 106, Lean, 20 weeks

description:
kidney cell 106
038s_F7


title: kidney cell 94, Lean, 20 weeks

description:
kidney cell 94
038s_F17


title: MGH170-P7-B02-CD45pos, Smart-seq2


title: kidney cell 96, Lean, 20 weeks

description:
kidney cell 96
038s_F19


title: kidney cell 104, Lean, 20 weeks

description:
kidney cell 104
038s_F5


title: kidney cell 93, Lean, 20 weeks

description:
kidney cell 93
038s_F16


title: MGH170-P7-A12-CD45pos, Smart-seq2


title: MGH170-P7-B09-CD45pos, Smart-seq2


title: MGH170-P7-A07-CD45pos, Smart-seq2


title: MGH170-P7-A11-CD45pos, Smart-seq2


title: kidney cell 95, Lean, 20 weeks

description:
kidney cell 95
038s_F18


title: MGH170-P7-A09-CD45pos, Smart-seq2


title: MGH170-P7-A08-CD45pos, Smart-seq2


title: MGH170-P7-A10-CD45pos, Smart-seq2


title: kidney cell 89, Lean, 20 weeks

description:
kidney cell 89
038s_F12


title: kidney cell 91, Lean, 20 weeks

description:
kidney cell 91
038s_F14


title: kidney cell 92, Lean, 20 weeks

description:
kidney cell 92
038s_F15


title: MGH170-P7-A02-CD45pos, Smart-seq2


title: kidney cell 86, Lean, 20 weeks

description:
kidney cell 86
038s_E9


title: MGH170-P7-A06-CD45pos, Smart-seq2


title: kidney cell 85, Lean, 20 weeks

description:
kidney cell 85
038s_E7


title: kidney cell 90, Lean, 20 weeks

description:
kidney cell 90
038s_F13


title: MGH170-P7-A01-CD45pos, Smart-seq2


title: Patient PARIS, pre-treatment sample, Chromium gene expression

library_source: transcriptomic single cell

data_processing:
We used CellRanger (v4.0.0) with the default parameters. Gene expression matrices were generated using cellranger (count command) by aligning the FASTQ files to a reference transcriptome.
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

source_name: Astrocytoma single nucleus (PARIS), PARIS_PRE

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics. IdhR132H mouse glioma cells with Notch1-KO and Notch1-WT were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks. The single-cell suspension for Notch1-KO and Notch1-WT mouse glioma cells treaded by AG-881 or DMSO (8,000 cells per group) were profiled by the 10X Chromium 3’ Single Cell Platform and were sequenced as already mentioned.
Single cells or single nucleus were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, 8,000 cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

value: No


title: kidney cell 84, Lean, 20 weeks

description:
kidney cell 84
038s_E6


title: MGH170-P7-A03-CD45pos, Smart-seq2


title: kidney cell 87, Lean, 20 weeks

description:
kidney cell 87
038s_F1


title: Patient BWH5033, post-treatment sample, Chromium gene expression

source_name: Astrocytoma single nucleus (BWH445), BWH5033_POST


title: kidney cell 82, Lean, 20 weeks

description:
kidney cell 82
038s_E4


title: kidney cell 88, Lean, 20 weeks

description:
kidney cell 88
038s_F11


title: kidney cell 83, Lean, 20 weeks

description:
kidney cell 83
038s_E5


title: Patient BWH445, on-treatment sample, Chromium gene expression

description: Chromium_Oligodendroglioma_processed_UMI.tsv

source_name: Oligodendroglioma single nucleus, BWH445_POST


title: kidney cell 81, Lean, 20 weeks

description:
kidney cell 81
038s_E3


title: MGH170-P7-A04-CD45pos, Smart-seq2


title: kidney cell 80, Lean, 20 weeks

description:
kidney cell 80
038s_E23


title: kidney cell 79, Lean, 20 weeks

description:
kidney cell 79
038s_E22


title: D1220-10_MOLM14_dnFOS_noDox

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Raw sequencing reads were trimmed to remove low quality sequences and adaptors using Trimmomatic v0.39 (Bolger et al. 014; PMID:24695404).
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.5 (Langmead et al. 2012; PMID:22388286) with the parameter --very-sensitive-local.
Potential PCR duplicates were identified and removed from alignments using the MarkDuplicates function in Picard tools v2.26.10 (https://broadinstitute.github.io/picard).
Peak calling was performed using MACS v2.2.7.1 (Zhang et al. 2008; PMID:18798982) using the option -B --trackline -q 0.01.
Assembly: hg38
Supplementary files format and content: BedGraph files of read pileups from MACS2

molecule: genomic DNA

growth_protocol: MOLM14 (DSMZ, ACC 777) were cultured in RPMI 1640 supplemented with 10% fetal calf serum, 2mM L-glutamine and 100 u/ml senicillin/streptomycin (all Gibco) at 37 ˚C with 5% CO2. Human embryonic kidney 293T (HEK293T) cells were cultured in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 0.11 mg ml–1 sodium pyruvate.

extract_protocol:
Double crosslinked cells were resuspended at 1x10^7 cells/ml in Buffer A (10 mM HEPES, 10 mM EDTA, 0.5 mM MEGTA, 0.25 % Triton- 100, 1x complete mini protease inhibitor cocktail (PIC) (Merck) pH 8.0) and incubated at 4 °C for 10 minutes prior to centrifugation at 500 xG for 10 min. This step was repeated with Buffer B (10 mM HEPES, 200 mM NaCl, 1 mM EDTA, 0.5 mM MEGTA, 0.01 % Triton-X 100, 1x PIC, pH 8.0) and after centrifugation 2 x 106 cells were resuspended in 300 μl IP buffer I (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 0.25 % SDS, 1x PIC, pH 8.0) and sonicated using a Diagenode Bioruptor Pico sonicator for 4 cycles (30 sec on 30 sec off) before centrifugation for 10 min at 16,000 xG. The supernatant was then collected and 600 μl IP Buffer II (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 7.5 % Glycerol, 1x PIC, pH 8.0) was added prior to immunoprecipitation. For immunoprecipitations 15 μl of Dynabeads-Protein G were washed twice with 500 μl 50 mM citrate phosphate buffer pH 5 and resupended in 15 μl citrate phosphate buffer with 4 μg anti-RUNX1 antibody (ab23980, Abcam) and 0.5% acetyl-BSA before incubation at 4 °C for 2 h. After incubation, dynabeads were washed with 500 μl pH 5 citrate phosphate buffer and resuspended in 15 μl citrate phosphate buffer with 0.5 % BSA before 555 μl of sonicated chromatin was added and incubated at 4 °C for ~ 16 h. After the incubation the dynabeads are washed sequentially with 500 μl of: Wash buffer 1 (20 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1% Triton-X 100, 0.1% SDS, pH 8.0) once, Wash buffer 2 (20 mM Tris-HCl, 500 mM NaCl, 20 mM EDTA, 1 % Triton-X 100, 0.1 % SDS, pH 8) twice, LiCl buffer (10 mM Tris-HCl,250 mM LiCl, 1 mM EDTA, 0.5 % NP-40, 0.5 % Na-deoxycholate, pH 8.0) once, TE/NaCl wash buffer (10 mM Tris-HCl, 50 mM NaCl, 1 mM EDTA, pH 8.0) twice. After these washes DNA was eluted from the dynabeads using 100 μl elution buffer (100 mM NaHCO3, 1% SDS). 200 mM NaCl and 500 μg/ml proteinase K were added to the eluant and the sample was reverse crosslinked at 65 °C for >4h. DNA was then purified by ampure (1.8x).
Libraries for next generation sequencing were prepared using a NebNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturers instructions. 16 cycles of PCR amplification were used and 200-450 bp fragments were size selected by gel electrophoresis. Libraries were validated by qPCR and quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to sequencing on a Nextseq 2000 75 using a NextSeq 500/550 High output kit.

treatment_protocol: Cells were treated with 1.5ug/ml doxycycline (+Dox) or no treatment  (no Dox) for 24 hours.

tag: cell line

value: FLT3-ITD AML

tag: antibody

value: ab23980, Abcam

tag: treatment


title: kidney cell 78, Lean, 20 weeks

description:
kidney cell 78
038s_E21


title: kidney cell 75, Lean, 20 weeks

description:
kidney cell 75
038s_E18


title: D1220-9_MOLM14_dnFOS_plusDox

value: Doxycycline


title: Patient BWH445, pre-treatment sample, Chromium gene expression

source_name: Oligodendroglioma single nucleus, BWH445_PRE


title: D1220-8_MOLM14_EV_noDox


title: D1220-7_MOLM14_EV_plusDox


title: kidney cell 76, Lean, 20 weeks

description:
kidney cell 76
038s_E19


title: Patient PARIS, post-treatment sample, Chromium gene expression

source_name: Astrocytoma single nucleus (PARIS), PARIS_POST


title: Patient BWH5033, pre-treament sample, Chromium gene expression

source_name: Astrocytoma single nucleus (BWH445), BWH5033_PRE


title: Cardio_9

city: Pamplona

first: Josune

last: Orbe

address: Avenida Pio XII 55

country: Spain

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR-2.7.0d with default parameters.
UMI deduplication was performed using UMI-tools v1.0.0
featureCounts v1.6.0 software and Gencode v38 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Plasma circulating extracellular vesicles

growth_protocol: Blood samples were collected in citrated tubes (Greiner Bio-one) and processed within 3.5 hours after mechanical thrombectomy. Citrated blood samples underwent two sequential centrifugations (Allegra X-30, Beckman Coulter), the first at 2000 x g for 10 minutes at 4ºC, and the second at 2500 x g for 15 minutes at 4ºC. The obtained platelet free plasma (PFP) was aliquoted and stored at -80ºC.

extract_protocol:
Medium/large size EVs were isolated from 400 μL of PFP diluted in 800 μL of filtered PBS (1x0.22 µm, followed by 1x0.1 µm filter) and centrifuged at 20,000 x g for 70 minutes at 4°C (Mikro 22R, Hettich Zentrifugen). The supernatant was carefully removed, and the pellet homogenized in filtered wash buffer (10 mM HEPES, 0.9% NaCl and 7.4 pH). A second centrifugation was performed (20,000 x g for 70 minutes at 4°C) and the pellet resuspended in 100 μL of filtered PBS, and stored at −80°C. Plasma EVs were separated by sequential centrifugation and resuspended in 100 μL of lysis/binding Buffer (Invitrogen). RNA transcripts were captured with Dynabeads oligo (dT) (Invitrogen) and reverse transcribed.
RNA samples underwent a linear amplification by in vitro transcription followed by a fragmentation into 250–350 bp. Partial Illumina adaptor sequences were used, and a second reverse transcription reaction was performed. Full Illumina adaptor sequences were successfully added and the libraries sequenced (NextSeq 2000, Illumina).

tag: is etiology

value: cardioembolic


title: Cardio_10

value: Plasma circulating extracellular vesicles


title: kidney cell 73, Lean, 20 weeks

description:
kidney cell 73
038s_E16


title: Atero_6

value: atherothrombotic


title: kidney cell 77, Lean, 20 weeks

description:
kidney cell 77
038s_E2


title: kidney cell 74, Lean, 20 weeks

description:
kidney cell 74
038s_E17


title: Atero_5


title: kidney cell 71, Lean, 20 weeks

description:
kidney cell 71
038s_E14


title: Cardio_8


title: kidney cell 70, Lean, 20 weeks

description:
kidney cell 70
038s_E13


title: Atero_4


title: Cardio_7


title: kidney cell 69, Lean, 20 weeks

description:
kidney cell 69
038s_E12


title: kidney cell 68, Lean, 20 weeks

description:
kidney cell 68
038s_E11


title: kidney cell 67, Lean, 20 weeks

description:
kidney cell 67
038s_E10


title: Cardio_5


title: kidney cell 66, Lean, 20 weeks

description:
kidney cell 66
038s_E1


title: kidney cell 65, Lean, 20 weeks

description:
kidney cell 65
038s_D7


title: ESUS_5

value: undetermined


title: Cardio_1


title: Cardio_4


title: kidney cell 64, Lean, 20 weeks

description:
kidney cell 64
038s_D5


title: Cardio_3


title: kidney cell 61, Lean, 20 weeks

description:
kidney cell 61
038s_D23


title: kidney cell 60, Lean, 20 weeks

description:
kidney cell 60
038s_D22


title: kidney cell 59, Lean, 20 weeks

description:
kidney cell 59
038s_D21


title: kidney cell 62, Lean, 20 weeks

description:
kidney cell 62
038s_D3


title: ESUS_3


title: kidney cell 72, Lean, 20 weeks

description:
kidney cell 72
038s_E15


title: kidney cell 55, Lean, 20 weeks

description:
kidney cell 55
038s_D18


title: Cardio_2


title: kidney cell 57, Lean, 20 weeks

description:
kidney cell 57
038s_D2


title: kidney cell 54, Lean, 20 weeks

description:
kidney cell 54
038s_D17


title: kidney cell 58, Lean, 20 weeks

description:
kidney cell 58
038s_D20


title: ESUS_4


title: ESUS_2


title: kidney cell 56, Lean, 20 weeks

description:
kidney cell 56
038s_D19


title: kidney cell 53, Lean, 20 weeks

description:
kidney cell 53
038s_D16


title: kidney cell 63, Lean, 20 weeks

description:
kidney cell 63
038s_D4


title: Atero_3


title: Cardio_6


title: Atero_1

value: IS atherothrombotic


title: SKMM1 (CUT&RUN2) IRF4 DMSO 2

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: CTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using BOTWIE2
Peaks were called by an inhouse program
Assembly: hg19
Supplementary files format and content: peak-read counts in wig format

source_name: cell line

growth_protocol: SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

extract_protocol:
DNA was extracted and processed following the Epicypher Cut&Run Kit protocol.
DNA libraries were prepared for sequencing using standard Epicypher protocols

treatment_protocol: The myeloma cell line  SKMM1 qA grown at 0.5 x 10^6 cells/ml and either treated with DMSO or 1000 nM AU15330 for 3 hours.  2 x 10^6 cells were collected for each sample.

value: cell line

tag: cell type

value: human multiple myeloma

tag: time

value: 3 hr

value: DMSO


title: SKMM1 (CUT&RUN2) IRF4 AU15330 2

description: TREATMENT


title: SKMM1 (CUT&RUN2) IRF4 AU15330 1

description: TREATMENT


title: ESUS_1


title: kidney cell 52, Lean, 20 weeks

description:
kidney cell 52
038s_D15

value: kidney

value: Lean

value: control

value: 20 weeks


title: kidney cell 51, Lean, 20 weeks

description:
kidney cell 51
038s_D14


title: Atero_2


title: SKMM1 (CUT&RUN2) ARID1A AU15330 1

description: TREATMENT


title: kidney cell 48, Lean, 20 weeks

description:
kidney cell 48
038s_D11


title: kidney cell 50, Lean, 20 weeks

description:
kidney cell 50
038s_D13


title: kidney cell 49, Lean, 20 weeks

description:
kidney cell 49
038s_D12


title: SKMM1 (CUT&RUN2) ARID1A AU15330 2

description: TREATMENT


title: kidney cell 46, Lean, 20 weeks

description:
kidney cell 46
038s_C9


title: kidney cell 47, Lean, 20 weeks

description:
kidney cell 47
038s_D10


title: SKMM1 (CUT&RUN1) NT 2

description: CTRL

treatment_protocol: A variant of the myeloma cell line SKMM1 carrying doxycyline-inducible Cas9  was  grown at 0.5 x 10^6 cells/ml and transduced with either non-targeting control or IRF4-targeting (#1 and #2) sgRNAs. One day after transduction cells were treated with doxcycline for 3 days followed by Cut&Run analysis.

value: 3 days

value: WT

value: non-targeting control sgRNA


title: SKMM1 (CUT&RUN1) IRF4 sg2 2

description: sgRNA 2

value: IRF4 Knockout

value: IRF4 sgRNA 2


title: kidney cell 43, Lean, 20 weeks

description:
kidney cell 43
038s_C5


title: kidney cell 44, Lean, 20 weeks

description:
kidney cell 44
038s_C6


title: SKMM1 (CUT&RUN2) ARID1A DMSO 1

description: CTRL


title: kidney cell 41, Lean, 20 weeks

description:
kidney cell 41
038s_C3


title: SKMM1 (CUT&RUN1) IRF4 sg1 2

description: sgRNA 1

value: IRF4 sgRNA 1


title: kidney cell 40, Lean, 20 weeks

description:
kidney cell 40
038s_C23


title: SKMM1 (CUT&RUN1) NT 1

description: CTRL


title: kidney cell 45, Lean, 20 weeks

description:
kidney cell 45
038s_C7


title: kidney cell 42, Lean, 20 weeks

description:
kidney cell 42
038s_C4


title: SKMM1 (CUT&RUN1) IRF4 sg2 1

description: sgRNA 2


title: kidney cell 39, Lean, 20 weeks

description:
kidney cell 39
038s_C22


title: SKMM1 (CUT&RUN1) IRF4 sg1 1

description: sgRNA 1


title: SKMM1 (CUT&RUN2) ARID1A DMSO 2

description: CTRL


title: NCIH929 isotype control 2

description: untreated, unstimulated cells

growth_protocol: NCIH929 and SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

treatment_protocol: The myeloma cell lines NCIH929 and SKMM1 were grown at 0.5 x 10^6 cells/ml over night.  2 x 10^6 cells were collected for each sample.

value: isotype ctrl

value: no time course

value: no treatment


title: kidney cell 38, Lean, 20 weeks

description:
kidney cell 38
038s_C21


title: NCIH929 isotype control 1

description: untreated, unstimulated cells

value: cell line


title: SKMM1 (CUT&RUN2) IRF4 DMSO 1

description: CTRL

value: human multiple myeloma


title: NCIH929 H3K27ac 1

description: untreated, unstimulated cells


title: NCIH929 H3K27ac 2

description: untreated, unstimulated cells


title: kidney cell 37, Lean, 20 weeks

description:
kidney cell 37
038s_C2


title: kidney cell 36, Lean, 20 weeks

description:
kidney cell 36
038s_C19


title: NCIH929 H3K4me3 2

description: untreated, unstimulated cells


title: kidney cell 35, Lean, 20 weeks

description:
kidney cell 35
038s_C18


title: NCIH929 H3K4me3 1

description: untreated, unstimulated cells


title: NCIH929 SMARCB1 2

description: untreated, unstimulated cells


title: kidney cell 34, Lean, 20 weeks

description:
kidney cell 34
038s_C17


title: NCIH929 SMARCB1 1

description: untreated, unstimulated cells


title: kidney cell 33, Lean, 20 weeks

description:
kidney cell 33
038s_C16


title: kidney cell 32, Lean, 20 weeks

description:
kidney cell 32
038s_C15


title: kidney cell 31, Lean, 20 weeks

description:
kidney cell 31
038s_C14


title: NCIH929 BRG1 1

description: untreated, unstimulated cells


title: kidney cell 28, Lean, 20 weeks

description:
kidney cell 28
038s_C10


title: NCIH929 MYC 2

description: untreated, unstimulated cells

value: MYC


title: NCIH929 ARID1A 2

description: untreated, unstimulated cells


title: NCIH929 BRG1 2

description: untreated, unstimulated cells


title: NCIH929 ARID1A 1

description: untreated, unstimulated cells


title: kidney cell 26, Lean, 20 weeks

description:
kidney cell 26
038s_B9


title: NCIH929 IRF4 2

description: untreated, unstimulated cells


title: kidney cell 27, Lean, 20 weeks

description:
kidney cell 27
038s_C1


title: kidney cell 25, Lean, 20 weeks

description:
kidney cell 25
038s_B7


title: NCIH929 IRF4 1

description: untreated, unstimulated cells


title: kidney cell 24, Lean, 20 weeks

description:
kidney cell 24
038s_B6


title: NCIH929 MYC 1

description: untreated, unstimulated cells


title: SKMM1 isotype control 2

description: untreated, unstimulated cells


title: kidney cell 23, Lean, 20 weeks

description:
kidney cell 23
038s_B5


title: SKMM1 isotype control 1

description: untreated, unstimulated cells


title: kidney cell 21, Lean, 20 weeks

description:
kidney cell 21
038s_B3


title: kidney cell 22, Lean, 20 weeks

description:
kidney cell 22
038s_B4


title: SKMM1 H3K27ac 2

description: untreated, unstimulated cells


title: SKMM1 H3K27ac 1

description: untreated, unstimulated cells


title: kidney cell 19, Lean, 20 weeks

description:
kidney cell 19
038s_B22


title: kidney cell 29, Lean, 20 weeks

description:
kidney cell 29
038s_C11


title: SKMM1 H3K4me3 2

description: untreated, unstimulated cells


title: SKMM1 SMARCB1 2

description: untreated, unstimulated cells


title: kidney cell 17, Lean, 20 weeks

description:
kidney cell 17
038s_B19


title: kidney cell 30, Lean, 20 weeks

description:
kidney cell 30
038s_C13


title: kidney cell 18, Lean, 20 weeks

description:
kidney cell 18
038s_B21


title: SKMM1 SMARCB1 1

description: untreated, unstimulated cells


title: SKMM1 BRG1 1

description: untreated, unstimulated cells


title: SKMM1 BRG1 2

description: untreated, unstimulated cells


title: kidney cell 15, Lean, 20 weeks

description:
kidney cell 15
038s_B17


title: kidney cell 16, Lean, 20 weeks

description:
kidney cell 16
038s_B18


title: kidney cell 13, Lean, 20 weeks

description:
kidney cell 13
038s_B14


title: SKMM1 ARID1A 1

description: untreated, unstimulated cells


title: kidney cell 11, Lean, 20 weeks

description:
kidney cell 11
038s_B12


title: SKMM1 MYC 1

description: untreated, unstimulated cells


title: kidney cell 10, Lean, 20 weeks

description:
kidney cell 10
038s_B11


title: kidney cell 12, Lean, 20 weeks

description:
kidney cell 12
038s_B13


title: SKMM1 ARID1A 2

description: untreated, unstimulated cells


title: SKMM1 IRF4 2

description: untreated, unstimulated cells


title: SKMM1 IRF4 1

description: untreated, unstimulated cells


title: kidney cell 9, Lean, 20 weeks

description:
kidney cell 9
038s_B10


title: kidney cell 20, Lean, 20 weeks

description:
kidney cell 20
038s_B23


title: NCIH929 4 hours (ATAC1) AU15330 2

description: TREATMENT

extract_protocol:
DNA was extracted following the Omni-ATACseq protocol published by Corces MR et al (Nat Methods, 2017).
DNA libraries were prepared for sequencing using standard Illumina protocols (Ceribelli M, et al. Cancer Cell, 2016).

treatment_protocol: The myeloma cell lines NCIH929 and SKMM1 were grown at 0.5 x 10^6 cells/ml and either treated with DMSO or 1000 nM AU15330 for 4 hours.  50 000 cells were collected for each sample.

value: 4 hr


title: kidney cell 7, Lean, 20 weeks

description:
kidney cell 7
038s_A8

value: kidney


title: kidney cell 8, Lean, 20 weeks

description:
kidney cell 8
038s_B1

value: Lean


title: SKMM1 H3K4me3 1

description: untreated, unstimulated cells


title: NCIH929 4 hours (ATAC1) AU15330 1

description: TREATMENT


title: NCIH929 4 hours (ATAC1) DMSO 2

description: CTRL

value: DMSO


title: kidney cell 6, Lean, 20 weeks

description:
kidney cell 6
038s_A3

value: control

value: 20 weeks


title: kidney cell 4, Lean, 20 weeks

description:
kidney cell 4
038s_A18


title: NCIH929 4 hours (ATAC1) DMSO 1

description: CTRL


title: kidney cell 5, Lean, 20 weeks

description:
kidney cell 5
038s_A21


title: SKMM1 4 hours (ATAC1) AU15330 2

description: TREATMENT


title: kidney cell 3, Lean, 20 weeks

description:
kidney cell 3
038s_A16


title: SKMM1 4 hours (ATAC1) AU15330 1

description: TREATMENT


title: SKMM1 MYC 2

description: untreated, unstimulated cells


title: kidney cell 14, Lean, 20 weeks

description:
kidney cell 14
038s_B15


title: kidney cell 1, Lean, 20 weeks

description:
kidney cell 1
038s_A1


title: NCIH929 4 hours (ATAC2) combination 2

description: TREATMENT

treatment_protocol: The myeloma cell lines NCIH929 and SKMM1 were grown at 0.5 x 10^6 cells/ml and either treated with DMSO, 50 nM FHD286, 50 nM trametinib, or combination (50 nM FHD286 PLUS 50 M trametinib) for 4 hours..  50 000 cells were collected for each sample.

value: 50 nM FHD286 + 50 nM trametinib


title: kidney cell 2, Lean, 20 weeks

description:
kidney cell 2
038s_A15


title: daHSC_d10_3

city: Bunkyo-ku

first: Taketomo

last: Kido

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
We used Bowtie2 (v2.2.5) to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM (v1.2.8) to calculate the gene expression level of each sample.
HISAT (v2.0.4) was used to align reads onto reference genome.
DESeq2 was used to identify DEGs.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-deliminated excel file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from qHSCs (day 0), aHSCs (day 7, day 10) and daHSCs (day 10) using the NucleoSpin RNA XS (MACHEREY-NAGAL, Duren, Germany), according to the manufacture’s protocol.
Libraries were prepared using the Optimal Dual-mode mRNA Library Prep Kit (BGI).

value: Day 10

value: deactivated hepatic stellate cells

value: WT

value: Hepatic stellate cell differentiation


title: daHSC_d10_2


title: NCIH929 4 hours (ATAC2) combination 1

description: TREATMENT


title: NCIH929 4 hours (ATAC2) Tranetinib 2

description: TREATMENT

value: 50 nM trametinib


title: aHSC_d10_3

value: activated hepatic stellate cells


title: NCIH929 4 hours (ATAC2) Trametinib 1

description: TREATMENT


title: aHSC_d10_2


title: aHSC_d10_1


title: NCIH929 4 hours (ATAC2) FHD286 2

description: TREATMENT

value: 50 nM FHD286


title: NCIH929 4 hours (ATAC2) DMSO 2

description: CTRL

value: cell line


title: NCIH929 4 hours (ATAC2) FHD286 1

description: TREATMENT

value: human multiple myeloma


title: aHSC_d7_3

value: Day 7


title: aHSC_d7_2


title: NCIH929 4 hours (ATAC2) DMSO 1

description: CTRL

value: 4 hr


title: aHSC_d7_1


title: SKMM1 4 hours (ATAC2) combination 2

description: TREATMENT


title: SKMM1 4 hours (ATAC1) DMSO 2

description: CTRL


title: qHSC_d0_3

value: Day 0

value: quiescent hepatic stellate cells


title: SKMM1 4 hours (ATAC1) DMSO 1

description: CTRL

value: DMSO


title: qHSC_d0_2


title: qHSC_d0_1


title: Parasrampuria_mRNA_Seq_shHD-33full_UAC_3

city: Winston-Salem

first: Keith

middle: T.

last: Gagnon

state: North Carolina

address: 575 Patterson Ave

department: Biochemistry and Molecular Biology

institute: Wake Forest University School of Medicine

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_shHD33fullUAC.csv

data_processing:
Sequenced reads were basecalled and demultiplexed using Dorado (v0.5.1).
Minimap2 alignment software was used to align demultiplexed reads to the GENCODE transcriptome reference Release 45 (GRCh38.p14).
Bam files were quantified using the Salmon RNA transcript quantification.
RNA-Seq data was analyzed using the DESeq2 (v1.42.1) package following the transcript abundance and tximport/tximeta input data format.
DESeq2 analysis codes are available in the supplementary file section.
GENCODE transcriptome reference Release 45 (GRCh38.p14)
Assembly: Parasrampuria_DESeq2_gene_counts.csv: Raw gene counts found using DESeq2 between sequenced samples using genes of interest.
Supplementary files format and content: Parasrampuria_Top_Gene_Change_Summary.csv: Top ten genes differentially expressed determined by greatest p-adj value normlaized to shMCHR control.
Supplementary files format and content: Parasrampuria_DESeq2_results_XXX.csv: DESeq2 results output to .csv with GeneIDs. Gene differentiation normalized to shMCHR control.

source_name: Coriell Institute HD fibroblasts (GM04281)

growth_protocol: HD fibroblasts were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Gibco), 1x non-essential amino acids (100X, Gibco), and 1% sodium pyruvate (100X, Gibco) at 37°C in 5% CO2.

extract_protocol:
Total RNA was Trizol extracted 7 days following infection and poly-A was isolated using magnetic bead purification methods.
The isolated mRNA was prepared using the cDNA-PCR Barcoding Kit V14 (Oxford Nanopore Technologies) following the manufacturers protocol and sequenced on a PromethION 2 Solo instrument (ONT).
RNA-Seq by cDNA-PCR, short read sequencing by Oxford Nanopore P2 Solo methods

treatment_protocol: Cells were infected with lentivirus vectors encoding smRNA at a MOI of 5 containing 1 ug/mL polybrene and incubated at 37°C in a humidified 5% CO incubator, changing media regularly.

value: Fibroblast

tag: biomaterial provider

value: HTT-Patient

value: Infection with lentiviral particles encoding smRNA


title: Rloop_N_2

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

data_processing:
Trim Galore was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Duplicated reads were removed using Picard MarkDuplicates.
Trimmed reads were aligned to the human hg19 reference genome using Bowtie2 with the default configuration
Definitions of R-loops by spKAS-seq were performed by following previously reported procedures (PMID: 36449625)
Assembly: hg19
Supplementary files format and content: bed files were genereated using bedtools by merging the peaks of two replicates
Supplementary files format and content: bw files were generated using deeptools
Library strategy: spKAS-seq

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
The purified genomic DNA was subsequently mixed with 5 μl of 20 mM dibenzocyclooctyne-PEG4-biotin conjugate (Sigma-Aldrich, 760749) and 10 μl of 10× phosphate-buffered saline (PBS), and the total volume was adjusted to 100 μl with 25 mM K3BO3. The resulting mixture was shaken gently at 37°C for 1.5 h, followed by addition of 5 μl of 10 mg/mL RNase A (Thermo Fisher Scientific, 12091039), and the mixture was shaken at 37°C for another 5 min. After the reaction, the DNA was isolated using the DNA Clean & Concentrator-5 kit (Zymo Research, D4013) and fragmented by sonication to 150 to 350 base pairs (bp). The sonicated DNA was employed for enrichment using 10 μl of Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001). The beads were washed with 1× binding and washing (B&W) buffer (5 mM tris-HCl, pH 7.4, 0.5 mM EDTA, 1 M NaCl, and 0.05% Tween 20), resuspended in 95 μl of 2× B&W buffer, and mixed with the sonicated DNA. The suspension was incubated at room temperature for 15 min. The beads were then washed once with 1× B&W buffer, twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal, and once again with 1× B&W buffer. The DNA was eluted from the beads by heating the beads in 10 μl H2O at 95°C for 10 min.
The ensuing enriched DNA and the corresponding input were employed for library construction using the Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a MGISEQ-2000 platform (BGI).
PROTOCOL: Strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq)

treatment_protocol: spKAS-seq was conduceted following previously published procedures with minor modifications (PMID: 36449625), where N2-heptynyl-dG was added to the culture medium until its final concentration reached 10 μM. After a 3-h incubation, the cells were treated with 5 mM N3-kethoxal dissolved in the culture medium for 10 min at 37°C, then harvested for genomic DNA isolation using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, K182002).

value: HEK293T cells

value: Human embryonic kidney

value: N2-heptynyl-dG  treatment


title: Parasrampuria_mRNA_Seq_shHD-33full_UAC_2

value: Coriell Institute HD fibroblasts (GM04281)


title: SKMM1 4 hours (ATAC2) Tranetinib 2

description: TREATMENT

value: 50 nM trametinib


title: daHSC_d10_1

value: Day 10

value: deactivated hepatic stellate cells

value: WT

value: Hepatic stellate cell differentiation


title: Parasrampuria_mRNA_Seq_shHD-33full_UAC_1


title: Parasrampuria_mRNA_Seq_shHD-33full_nb_3

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_shHD33fullnb.csv


title: Rloop_2


title: SKMM1 4 hours (ATAC2) combination 1

description: TREATMENT

value: cell line

value: human multiple myeloma

value: 50 nM FHD286 + 50 nM trametinib